JOURNAL OF BACTERIOLOGY, May 2006, p. 3365–3370
Copyright © 2006, American Society for Microbiology. All Rights Reserved.
Vol. 188, No. 9
A Distinct QscR Regulon in the Pseudomonas aeruginosa
Yannick Lequette,1Joon-Hee Lee,1Fouzia Ledgham,2Andre ´e Lazdunski,2and E. Peter Greenberg1*
Department of Microbiology, University of Washington, Seattle, Washington 98195,1and Laboratoire d’Inge ´nierie des
Syste `mes Macromole ´culaires, IBSM/CNRS, Marseille 13402, Cedex 20, France2
Received 12 October 2005/Accepted 1 February 2006
The opportunistic pathogen Pseudomonas aeruginosa possesses two complete acyl-homoserine lactone (acyl-
HSL) signaling systems. One system consists of LasI and LasR, which generate a 3-oxododecanoyl-homoserine
lactone signal and respond to that signal, respectively. The other system is RhlI and RhlR, which generate
butanoyl-homoserine lactone and respond to butanoyl-homoserine lactone, respectively. These quorum-sensing
systems control hundreds of genes. There is also an orphan LasR-RhlR homolog, QscR, for which there is no
cognate acyl-HSL synthetic enzyme. We previously reported that a qscR mutant is hypervirulent and showed
that QscR transiently represses a few quorum-sensing-controlled genes. To better understand the role of QscR
in P. aeruginosa gene regulation and to better understand the relationship between QscR, LasR, and RhlR
control of gene expression, we used transcription profiling to identify a QscR-dependent regulon. Our analysis
revealed that QscR activates some genes and represses others. Some of the repressed genes are not regulated
by the LasR-I or RhlR-I systems, while others are. The LasI-generated 3-oxododecanoyl-homoserine lactone
serves as a signal molecule for QscR. Thus, QscR appears to be an integral component of the P. aeruginosa
quorum-sensing circuitry. QscR uses the LasI-generated acyl-homoserine lactone signal and controls a specific
regulon that overlaps with the already overlapping LasR- and RhlR-dependent regulons.
The opportunistic pathogen Pseudomonas aeruginosa can be
found free living in water and soil. This bacterium also causes
infections in a variety of animals and plants (7). Quorum-
sensing systems control hundreds of P. aeruginosa genes, in-
cluding genes that code for exoenzymes and extracellular vir-
ulence factor synthesis. Quorum sensing also plays a role in
biofilm development (4, 5, 13, 17, 22, 28). There are two well-
studied P. aeruginosa acyl-homoserine lactone (acyl-HSL) quo-
rum-sensing systems. One system is comprised of the LasR
signal receptor, which responds to the LasI-generated signal
N-3-oxododecanoyl-homoserine lactone (3OC12-HSL). The
other system is comprised of the RhlR signal receptor, which
responds to the RhlI-generated signal N-butanoyl-homoserine
lactone (C4-HSL) (5, 13, 18, 19, 26, 29). The rhlI and rhlR
genes are among the functions activated by LasR and LasI.
Both systems are also integrated in regulatory networks that
In addition to LasR and RhlR, there is a third, orphan
LasR-RhlR homolog, QscR, for which there is no cognate
acyl-HSL synthase gene (3). A qscR mutant is hypervirulent.
The influence of QscR on the expression of a few genes con-
trolled by the LasR-I and RhlR-I systems has been examined.
These genes are prematurely activated in a qscR mutant and
include genes in the phz1 and phz2 phenazine synthesis oper-
ons; hcnAB, the hydrogen cyanide synthesis operon; lasB,
which codes for elastase; rhlI; and lasI (3, 14). The mechanism
for transient repression of these genes by QscR is not clear. At
low acyl-HSL concentrations, QscR can form heterodimers
with LasR and RhlR. This might inactivate LasR and RhlR (3,
14). It is also possible that QscR sequesters acyl-HSL signals
and thereby delays the expression of LasR- and RhlR-depen-
dent genes (3, 14). To develop a better view of the role of QscR
in P. aeruginosa gene regulation, we employed microarray tech-
nology to assess the influence of QscR on the transcriptome.
We show that QscR affects transcript levels of over 400 genes,
most of which are not affected by the LasR-I or RhlR-I sys-
tems. Our microarray studies and subsequent reporter gene
experiments indicate that there is a specific QscR regulon. We
believe that QscR can directly influence specific genes in re-
sponse to the LasI-generated signal 3OC12-HSL.
MATERIALS AND METHODS
Bacterial strains and plasmids. We used the isogenic P. aeruginosa strains
PAO1 and PAO-R3 (3), and we used Escherichia coli DH5?. The P. aeruginosa
strains overexpressing qscR (YL113) and a qscR 3? deletion (YL117) were con-
structed in PAO-R3 as follows. A qscR overexpression plasmid (pJN105-QscR)
was constructed as described elsewhere previously (15). An in-frame deletion of
the qscR 3? end was created as follows. We amplified an XbaI-SacI fragment
extending from 45 bp upstream of the qscR start codon through codon 182
(PCR-1). We amplified a second SacI-XbaI fragment extending from codon 219
to 67 bases past the stop codon (PCR-2). The PCR-1 and PCR-2 products were
cloned together into XbaI-digested pJN105 to yield a plasmid coding for a QscR
DNA-binding mutant polypeptide missing amino acid residues 183 to 218
(pYL135). The SalI-SacI (with the SacI site blunt ended) fragment from pJN105-
QscR and the SalI-NotI fragment (with the NotI site blunt ended) from pYL135
were cloned into SalI-SspI-digested mini-CTX-lacZ to yield pYL129 and
pYL137. These plasmids were used to insert qscR alleles into the P. aeruginosa
chromosomal attB site by standard techniques (10, 11). The resulting P. aerugi-
nosa strains had unmarked chromosomal copies of a qscR allele. All primers used
in this study are described in Table S1 in the supplemental material.
Plasmids with point mutations in qscR were constructed with PCR products as
follows. Mutations were constructed in two PCR steps. The first PCR used one
flanking primer and an internal primer containing a point mutation. The second
PCR used the other flanking primer and a complementary internal primer with
* Corresponding author. Mailing address: Department of Microbi-
ology, HSB Room G-328, 1959 NE Pacific Street, Seattle, WA 98195-
7242. Phone: (206) 616-2881. Fax: (206) 616-2938. E-mail: epgreen@u
† Supplemental material for this article may be found at http://jb
the desired point mutation. Gel-purified PCR fragments were annealed and
amplified by PCR using flanking primers, which included XbaI overhangs. The
resulting PCR product was digested with XbaI and cloned into pJN105. The
Microarray analysis. All strains were grown under identical conditions in
Luria-Bertani (LB) broth containing 50 mM MOPS (morpholinepropanesulfonic
acid) (pH 7.0) as described elsewhere previously (22), except that we included
0.2% L-arabinose in every case. We isolated RNA from 2 ? 109cells from
cultures at optical densities at 600 nm of 0.5, 0.8, 1.4, 2.0, and 3.5. The RNA
purification, cDNA synthesis, fragmentation, labeling, and processing of P.
aeruginosa microarrays (Affymetrix) were performed as described previously
(22). Experiments with strains PAO1 and PAO-R3 were done in duplicate.
Experiments with strains YL113 and YL117 were done once. Data were pro-
cessed with Affymetrix software suite 1.1, CYBER-T (http://www.visitor.ics.uci
.edu/genex/cybert/) (1, 8), and GeneSpring 6.1. To identify those genes with
expression significantly different between PAO1 and PAO-R3 at different culture
densities, we used CYBER-T. The Bayesian prior estimate was 10, and the
sliding-window size was 101. The P value threshold was 0.001, the posterior proba-
bility of differential expression was ?0.95, and the severalfold change was ?2.5.
Real-time PCR. Primers (see Table S1 in the supplemental material) were
designed using Primer Express software (Taqman). Total RNA was extracted
from P. aeruginosa cultures at optical densities (600 nm) of 0.4, 1, 2.0, 3.0, and
4.0. PCRs included 1 ng of cDNA, and primers at a concentration of 300 nM in
25 ?l of SYBR green PCR amplification master mix (Applied Biosystems).
Real-time PCR conditions were as follows: 2 min at 50°C, 10 min at 95°C, 40
cycles of 15 s at 95°C (denaturation step), and 1 min at 60°C (annealing and
extension steps). Genomic DNA was used as a standard, and nadB (PA0761) was
used as an internal control.
Measurement of lacZ transcription in recombinant E. coli. To monitor lacZ
transcription, we measured ?-galactosidase activity by using a Galacto-Light Plus
kit (Tropix) as described elsewhere previously (28). Results are given in units of
?-galactosidase per optical density at 600 nm.
Microarray accession number. Microarray analysis data have been deposited
in the GEO database (http://www.ncbi.nlm.nih.goc/geo) under accession number
The P. aeruginosa QscR regulon. We first compared tran-
scriptomes of the P. aeruginosa PAO-R3 qscR mutant and the
parental strain, PAO1, at several points during growth (optical
density at 600 nm of 0.5, 0.8, 1.4, 2.0, and 3.5). We identified
424 genes and eight intergenic regions showing statistically
significant differences of at least 2.5 (see Tables S2, S3, and S4
in the supplemental material). Most of the 424 differentially
regulated genes appeared to be repressed by QscR (329
genes), but 76 genes appeared to be induced by QscR. Nine-
teen genes were discontinuously regulated during growth. We
assume that the discontinuously regulated genes are controlled
via multiple inputs, with QscR representing one input.
Our transcriptome analysis and real-time PCR analyses con-
firmed previous reports (3, 14) that QscR repressed hcnABC
and the two phenazine operons (phzI and phzII) in logarithmic
phase. Moreover, we found that QscR induced hcnA in sta-
tionary phase and repressed lasB until early stationary phase.
We grouped the QscR-controlled genes into five classes based
on the timing of QscR-dependent regulation (Fig. 1; see Tables
S2 to S4 in the supplemental material): there are 98 class I
genes regulated by QscR in exponential phase, 195 class II
genes showing differential transcript levels during the transi-
tion from logarithmic to stationary phase, 94 class III genes
regulated by QscR in stationary phase, 18 class IV genes reg-
ulated at all times during growth, and 19 class V genes showing
discontinuous regulation during growth.
Role of the QscR DNA-binding domain in regulation of gene
expression. The formation of inactive QscR-LasR and QscR-
RhlR heterodimers cannot explain the QscR activation we
observed in our transcriptome analysis, nor can it explain the
QscR repression of genes that are not regulated by the LasR-I
or RhlR-I systems. Rather, our observations suggest that QscR
might be capable of binding to certain promoters directly. The
QscR protein has a DNA-binding domain and an acyl-HSL
recognition domain (3). We predicted that a mutant QscR with
a defect in the DNA-binding domain might retain an ability to
repress genes by forming heterodimers with LasR or RhlR or
by sequestering acyl-HSLs, but it should not be able to control
gene expression by a direct interaction with promoters. Thus,
we constructed P. aeruginosa qscR mutants containing a chro-
mosomal copy of either an L-arabinose promoter-driven qscR
allele (pbad-qscR) or an L-arabinose promoter-driven qscR de-
letion that codes for a polypeptide with a truncation of the
C-terminal DNA-binding domain (pbad–qscR-?dbd) (see Ma-
terials and Methods). Under the conditions of our experi-
ments, the L-arabinose promoter-controlled qscR alleles were
both expressed at a level about 50-fold higher than that of qscR
in the parental strain, PAO1 (data not shown). We identified
38 genes (Table 1) that were at least threefold differentially
expressed in the strain containing the L-arabinose promoter-
driven qscR allele compared to the strain containing the L-
arabinose promoter-driven qscR-?dbd allele and were also at
least threefold differentially expressed in the parent strain,
PAO1, compared to the strain containing the qscR null muta-
tion. We suspect that QscR controls at least some of these 38
genes directly. There are many other ways to sort these genes.
We chose this analysis as a way to derive a minimum number
of genes with some likelihood of being controlled by QscR
Evidence for direct control of PA1897 by QscR and 3OC12-
HSL. To provide further evidence that QscR can regulate P.
aeruginosa genes directly, we studied PA1897 gene expression
in recombinant E. coli (Table 2). We chose PA1897 because we
found that in P. aeruginosa PA1897, transcript levels were low
in the qscR null mutant, higher in the wild type, and even
higher in the qscR overexpression strain (Fig. 2). Furthermore,
PA1897 is adjacent to qscR on the P. aeruginosa genome (24),
it requires 3OC12-HSL for full induction (22), and LasR does
not bind to the PA1897 promoter (23). Expression of a plas-
mid-encoded PA1897-lacZ fusion was relatively low in the
absence of both a plasmid expressing qscR and added 3OC12-
HSL (Table 2). In the presence of both QscR and 3OC12-HSL,
lacZ expression was nearly 200-fold higher than that in the
absence of QscR. LasR did not substitute for QscR, and C4-
HSL did not substitute for 3OC12-HSL.
We also used five distinct qscR alleles containing single point
mutations in codons for amino acid residues conserved in
LuxR homologs or conserved in the 3OC12-HSL recognition
region of LasR (12). None of the QscR point mutant polypep-
tides activated the PA1897-lacZ reporter (Table 2). The QscR-
dependent activation of the PA1897 promoter is consistent
with a model of direct QscR function. Our experiments further
indicate that QscR, which does not have a cognate acyl-HSL
synthase, recognizes the 3OC12-HSL signal from the LasR-
Relationships between the QscR, LasR, and RhlR regulons.
Several groups have previously used microarrays to identify
genes controlled by the LasR-LasI and RhlR-RhlI systems (9,
3366LEQUETTE ET AL. J. BACTERIOL.
FIG. 1. GeneSpring cluster analysis of P. aeruginosa QscR-regulated genes and examples of transcript levels for members of each class of
expression pattern at different culture densities. (A) Cluster analysis. Red indicates negative changes in transcript levels of the parent compared
to the qscR null mutant, and green indicates positive changes in transcript levels of the parent compared to the qscR null mutant. Class I, genes
regulated in logarithmic phase; class II, genes regulated during the transition from logarithmic to stationary phase; class III, genes regulated in
stationary phase; class IV, genes regulated throughout growth; class V, genes discontinuously regulated. (B) Transcript levels (?1,000; units as
determined by array software) for representative members of each class. Transcript levels of the qscR null mutant (E) and wild type (ƒ) are shown.
The gene numbers or gene names are indicated according to the Pseudomonas Genome Project website (http://www.pseudomonas.com).
VOL. 188, 2006 THE PSEUDOMONAS AERUGINOSA QscR REGULON 3367
22, 25). We used experimental conditions comparable to those
described previously by Schuster et al. (22) for our array ex-
periments. Thus, we have compared our data to those de-
scribed previously by Schuster et al. (22). We found that only
37% of the QscR regulon is activated (159 genes) by the
LasR-I or RhlR-I systems. Among the 159 genes, only 12% (19
genes) were induced by QscR. All 19 of these genes depend
primarily on 3OC12-HSL for expression and show little or no
additional activation by C4-HSL (Fig. 3A) (22). Eight of the
nine genes discontinuously regulated by QscR during growth
require C4-HSL for full activation (data not shown).
QscR repressed 131 LasR-I- or RhlR-I-activated genes identi-
fied previously (22). Of these genes, 48% require C4-HSL for
activation, 36% require both 3OC12-HSL and C4-HSL for max-
imal activation, and 16% require 3OC12-HSL only for activation
(Fig. 3B). The six previously identified quorum-sensing genes
repressed by QscR (3, 14) belong to a subset of 38 genes
affected by QscR in the logarithmic phase. An example of
transcript levels during growth for a gene in this subset is
shown in Fig. 1B (class I). QscR represses other genes later in
growth (classes II to V) (Fig. 1B). Genes activated by the
RhlR-I or LasR-I systems and repressed by QscR, particularly
those genes repressed by QscR in logarithmic phase, may be
affected by the ability of QscR to form heterodimers with RhlR
or LasR or by an ability to sequester acyl-HSL signals, but we
cannot rule out the possibility of direct regulation of some of
these genes at this time.
Functional classification of QscR-regulated genes. Functional
classification was based on the Pseudomonas Genome Project
FIG. 2. Transcript levels of PA1897-1894 in the P. aeruginosa par-
ent strain and in P. aeruginosa qscR mutants. The qscR mutants are the
qscR null mutant, the strain expressing L-arabinose promoter-driven
qscR (pbad-qscR), and the strain expressing the L-arabinose promoter-
driven qscR deletion that codes for a polypeptide with a truncation of
the C-terminal DNA-binding domain (pbad-qscR-?dbd). Transcript
levels from cultures at an optical density (600 nm) of 1.4 are the
averages of transcript levels for PA1897, PA1895, and PA1894 open
reading frames from our microarray data. Errors bars show the stan-
TABLE 1. Genes potentially dependent on the native
DNA-binding domain of QscR
Conserved hypothetical protein
pcaH; aromatic compound
pcaG; aromatic compound
Conserved hypothetical protein
Conserved hypothetical protein
Conserved hypothetical protein
Conserved hypothetical protein
Conserved hypothetical protein
Glycine, serine and threonine
ilvA2; glycine, serine, and
Conserved hypothetical protein
Probable glycogen synthase
Probable dehydrogenase E1
Conserved hypothetical protein
Probable rubredoxin reductase
rubA1; rubredoxin reductase
PA1326 3.6 (1.4)
aPA gene number, gene name, and description are according to the Pseudo-
monas Genome Project website (http://www.pseudomonas.com).
bExpression levels in the strain overexpressing pbad-qscR compared with the
strain overexpressing pbad-qscR-?dbd. Values in parentheses are optical densi-
ties at which maximum changes were observed.
cGenes regulated by the LasR-I or RhlR-I systems as determined elsewhere
TABLE 2. Acyl-HSL-dependent expression of a PA1897-lacZ
fusion in E. coli containing LasR, QscR, or QscR mutant
?-Galactosidase activities (U)
79 ? 34
86 ? 24
95 ? 43
57 ? 28
77 ? 50
89 ? 40
77 ? 40
75 ? 20
88 ? 47
91 ? 33
73 ? 34
65 ? 16
85 ? 2318,500 ? 2,500
50 ? 26
175 ? 40
75 ? 34
180 ? 90
75 ? 20
aAll strains carried the PA1897-lacZ reporter pJL101 with the indicated qscR
or lasR expression plasmid. The control vector is pJN105; pJN105-LasR, called
pJN105L previously by Lee et al. (15) contained lasR; pJN105-QscR contained
wild-type qscR; and the other plasmids contained qscR with point mutations
coding for substitutions in the amino acid residues indicated. Transcription from the
PA1897 promoter was assessed by measuring ?-galactosidase activity in cells from
cultures at an optical density at 600 nm of 1.8 to 2.0. Values are the means ?
standard deviations of three individual experiments.
3368LEQUETTE ET AL. J. BACTERIOL.
website (http://www.pseudomonas.com). The main classes rep-
resented in the QscR regulon were energy source metabo-
lism (13%), transport of small molecules (11%), and virulence
factor biosynthesis (9%) (see Fig. S1A in the supplemental
material). QscR did not regulate any genes involved in cell
division, cell wall/lipopolysaccharide/capsule, or nucleotide
biosynthesis and metabolism (see Fig. S1A in the supplemental
material). QscR repressed some genes and activated some
genes in almost every class (see Fig. S1B in the supplemental
material). The exceptions were genes coding for production of
secreted factors and quinolone biosynthesis genes. Genes in
these two groups were repressed but not activated by QscR and
are only activated by LasR and RhlR (22). QscR repressed 31
iron starvation response cistrons.
Previous studies have shown that the orphan LasR-RhlR
homolog QscR can influence the virulence of P. aeruginosa. A
qscR mutant was hypervirulent. Furthermore, QscR was shown
to delay the expression of several genes that were activated by
LasR or RhlR (3, 14). There are several possible explanations
for these QscR phenotypes: QscR might interact with specific
LasR- or RhlR-controlled promoters directly; QscR might
bind to the LasR signal, 3OC12-HSL, or the RhlR signal,
C4-HSL; or QscR might form inactive heterodimers with LasR
or RhlR. In fact, evidence indicates that QscR can form het-
erodimers with LasR and RhlR (14). Heterodimer formation
could explain the QscR delays in expression of several LasR-
and RhlR-activated genes. There is precedent for this type of
regulatory effect. In Agrobacterium tumefaciens, there is a ho-
molog of the quorum-sensing signal receptor TraR. This ho-
molog, TrlR, is an orphan TraR homolog that, unlike QscR,
has a mutation that eliminates its DNA-binding region. Thus,
it can function only in the capacity of forming inactive het-
erodimers or sequestering signal (2, 16, 31).
The proposed functions of QscR are not exclusive of each
other, and because, unlike the A. tumefaciens TrlR, QscR has
what appears to be a functional DNA-binding domain, it could
function via direct binding to specific promoter elements. To
investigate the mechanisms by which QscR might influence P.
aeruginosa gene expression, we compared the transcriptomes of a
qscR mutant, a mutant that overexpresses QscR, a mutant that
overexpresses a defective QscR with a deletion in the C-terminal
DNA-binding domain, and the parent. Our results show that
QscR can activate some genes and repress some genes that are
not regulated by the LasR-I or RhlR-I systems. The regulation
of these genes must not result from the formation of inactive
LasR-QscR or RhlR-QscR dimers or from QscR competition
for acyl-HSLs with LasR or RhlR. Many QscR-activated genes
show higher levels of transcription in the QscR overexpression
strain than in the parent (and higher levels in the parent than
in the qscR null mutant). This indicates that QscR levels are
limiting in the wild type under the conditions of our experi-
As a confirmation that QscR can activate P. aeruginosa genes
directly, we studied the influence of QscR on the expression of
one gene (PA1897) selected from among those activated by
QscR in recombinant E. coli (Table 2). Although PA1897 has
a 20-bp inverted repeat promoter element similar to those
involved in the activation of some LasR-dependent genes,
LasR does not bind to this element (23). In fact, PA1897 shows
a strong 3OC12-HSL-dependent induction by QscR in E. coli.
The substitution of C4-HSL for 3OC12-HSL is ineffective, as
was the substitution of LasR for QscR. Our parallel work on
purified QscR shows that in vitro, this transcription factor
binds to the PA1897 inverted repeat element in a 3OC12-HSL-
dependent manner (15). All of this information is consistent
with the conclusion that QscR is a 3OC12-HSL-responsive
transcription factor that is capable of binding to and affecting
specific promoters in P. aeruginosa. It now seems evident that
our previous demonstration of a small activation of the
PA1897 promoter in E. coli overexpressing LasR (27) was not
a reflection of promoter specificity in P. aeruginosa. Rather, it is
analogous to the activation of the lasB promoter in recombinant
E. coli overexpressing the Vibrio fischeri LuxR protein (6).
Although we have learned some things about the signal-
binding specificity and DNA-binding specificity of QscR from
our transcriptome analysis and our in vitro analysis of QscR
(15), some important issues remain to be resolved. We cannot
yet conclude what genes other than those described previously
(15) possess QscR-binding sites. We have not succeeded to
learn more about binding targets by using computational ap-
proaches (Y. Lequette and E. P. Greenberg, unpublished
data). In view of recent discoveries that the promoter regions
of LasR-controlled genes do not always have sequence simi-
larity to each other (23), this comes as no surprise. We previ-
ously suggested (15) that QscR might function to recognize
signals produced by other bacteria. This was based on the fact
the QscR was slightly more sensitive to 3OC10-HSL than it
was to 3OC12-HSL. We have little to add in this regard. The
alternative is that QscR was acquired relatively recently by
horizontal gene transfer and that it has evolved to a point
where it now functions to respond to 3OC12-HSL and control
specific genes in response to P. aeruginosa population density.
We have not performed any experiments involving coculture of
P. aeruginosa with a 3OC10-HSL- or a C10-HSL-producing
Many transcripts that are influenced by overexpressed QscR
FIG. 3. Venn diagrams showing overlaps between QscR-repressed
and QscR-activated genes and LasR-I and RhlR-I regulons. Blue,
genes that require LasR-I for activation; yellow, genes that require
RhlR-I for activation; gray, genes that require both LasR-I and RhlR-I
for activation. (A) Green, QscR-activated genes. (B) Pink, QscR-
repressed genes. There are an additional 274 QscR-dependent genes
that are not induced by the LasR-I or RhlR-I systems and are not
represented in these Venn diagrams.
VOL. 188, 2006THE PSEUDOMONAS AERUGINOSA QscR REGULON3369
are also influenced by the overexpressed QscR DNA-binding
domain mutant polypeptide. We believe that QscR regulates
the genes encoding these transcripts indirectly. This indirect
effect could result from heterodimer formation, by competition
of QscR with LasR for 3OC12-HSL or with RhlR for C4-HSL,
by both mechanisms, or in some unexplained nonspecific
We are left with the view that QscR affects the transcription
of well over 7% of the more than 5,500 genes in the P. aerugi-
nosa genome. Many of these genes are regulated by the LasR-
LasI and RhlR-RhlI quorum-sensing systems and may be in-
fluenced by QscR indirectly. Others appear to be regulated by
QscR together with the LasR-LasI signal 3OC12-HSL directly.
Furthermore, like rhlR, qscR activity is regulated by the LasR-
LasI quorum-sensing system. In the case of rhlR, LasR func-
tions at the level of transcription. In the case of QscR, the
LasR-LasI system dominates, because QscR requires the LasI-
generated quorum-sensing signal 3OC12-HSL for direct con-
trol of gene expression. We conclude that QscR, LasR, and
RhlR control overlapping but distinct regulons in P. aeruginosa
and that QscR is capable of direct activation of a group of P.
This study was supported by USPHS grant GM-59026 and by a grant
from the W. M. Keck Foundation.
We thank Jessica Linton from the University of Iowa DNA core
facility for microarray processing.
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