Previous Article | Next Article 
Microbiology and Molecular Biology Reviews, September 2004, p. 474-500, Vol. 68, No. 3
1092-2172/04/$08.00+0 DOI: 10.1128/MMBR.68.3.474-500.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.
Bacterial Transcriptional Regulators for Degradation Pathways of Aromatic Compounds
David Tropel1 and Jan Roelof van der Meer1,2*
Swiss Federal Institute for Environmental Science and Technology (EAWAG), Dübendorf,1
Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland2

SUMMARY
Human activities have resulted in the release and introduction
into the environment of a plethora of aromatic chemicals. The
interest in discovering how bacteria are dealing with hazardous
environmental pollutants has driven a large research community
and has resulted in important biochemical, genetic, and physiological
knowledge about the degradation capacities of microorganisms
and their application in bioremediation, green chemistry, or
production of pharmacy synthons. In addition, regulation of
catabolic pathway expression has attracted the interest of numerous
different groups, and several catabolic pathway regulators have
been exemplary for understanding transcription control mechanisms.
More recently, information about regulatory systems has been
used to construct whole-cell living bioreporters that are used
to measure the quality of the aqueous, soil, and air environment.
The topic of biodegradation is relatively coherent, and this
review presents a coherent overview of the regulatory systems
involved in the transcriptional control of catabolic pathways.
This review summarizes the different regulatory systems involved
in biodegradation pathways of aromatic compounds linking them
to other known protein families. Specific attention has been
paid to describing the genetic organization of the regulatory
genes, promoters, and target operon(s) and to discussing present
knowledge about signaling molecules, DNA binding properties,
and operator characteristics, and evidence from regulatory mutants.
For each regulator family, this information is combined with
recently obtained protein structural information to arrive at
a possible mechanism of transcription activation. This demonstrates
the diversity of control mechanisms existing in catabolic pathways.

INTRODUCTION
Human activities have resulted in the release and introduction
into the environment of a plethora of aromatic chemicals. Although
the input of these synthetic chemicals may be smaller than the
total amount of aromatic compounds released from decaying plant
material, their novel structures or their quantities as single
pure molecules induce major changes in microbial communities,
which are the major recyclers of organic chemicals in nature
(
76). For example, large quantities of a single organic solvent
offer a very specific metabolizable carbon source for specialized
groups of microorganisms (
161) and thus can act selectively
for enrichment of those groups in the environment (
87,
154).
Compounds such as chlorinated solvents, herbicides, and pesticides
often carry uncommon chemical structures, side chains, or functional
groups, which can have toxic effects or provide new carbon sources
for bacteria which have adapted their metabolism to degrade
the compounds (
191,
207,
261). The interest in discovering how
bacteria are dealing with hazardous environmental pollutants
has driven a large research community and has resulted in important
biochemical, genetic, and physiological knowledge about the
degradation capacities of microorganisms (
40,
43,
76,
146,
191,
206,
207). A large variety of metabolic pathways have been discovered
in very different microorganisms, fueling up-to-date online
databases such as the Biocatalysis/Biodegradation Database (
57).
Knowledge about the biodegradation capacities of microorganisms
is being applied directly in bioremediation practice (
240),
and individual biotransformation reactions are potentially very
interesting for incorporation into chemical synthesis (
230).
Less obviously associated with bioremediation applications, green chemistry, or production of pharmacy synthons have been studies of the regulatory mechanisms, which govern the expression of specific catabolic pathways (105). However, regulation of catabolic pathway expression has attracted the interest of numerous different groups, who have tried to unravel the molecular partners in the regulatory process, the signals triggering pathway expression, and the exact mechanisms of activation and repression. More recently, information about regulatory systems has attracted interest, with the potential of these systems being used as sensory mechanisms in whole-cell living bioreporters, genetically modified bacteria which can be used as sensors to measure the quality of aqueous, soil, and air environments (49, 96, 242). It soon was discovered that a large diversity of regulatory systems existed for mediating the expression of catabolic pathways. Furthermore, many related catabolic pathways did not carry the same regulatory system, which led to the hypothesis that regulatory systems and their target operons do not necessarily coevolve but seem to become associated independently (23, 39). As genomic, genetic, and biochemical data accumulated, regulatory proteins for catabolic gene expression were classified into other protein families, showing that they (as expected) were not unique to typical biodegradation pathways per se. In fact, many aromatic degradation pathways, typically those involved in the metabolism of aromatic amino acids, hydroxylated benzoates and phenylpropionic acids, ubiquinones, and aromatic amines, are very widespread among microbial species (43), leaving perhaps only the catabolic pathways for toxic and xenobiotic compounds to the groups of microorganisms usually considered for biodegradation (i.e., pseudomonads, sphingomonads, Rhodococcus spp., Ralstonia spp., and Burkholderia spp.). One would thus have to conclude that the capabilities of regulatory proteins to react specifically to substrates or intermediates of catabolic pathways have evolved many times independently; this is explained in more detail below.
Although excellent reviews exist on the diversity of catabolic pathways (76, 206), on evolutionary aspects (99, 262, 271), and on different details of specific regulator families (71, 139, 224, 233), no concise overview of the different regulatory systems involved in biodegradation pathways (or catabolic pathways, as we will refer to them often) exists in the literature, although a shorter treatise was published by Diaz and Priets (44). In our opinion, the topic of biodegradation is relatively coherent, and thus treatment of the different regulatory systems involved in catabolic pathways also deserves a coherent overviewalthough it is clear that there are no special "catabolic" regulatory proteins. In addition, several three-dimensional structures of regulatory proteins have recently been resolved, which allows a much more detailed prediction of how the actual activation and repression mechanisms of regulatory proteins take place. This might solve many questions which have arisen from more traditional genetic and biochemical approaches to transcription activation and repression. The current view of regulatory proteins is that of a set of sophisticated protein-DNA-RNA polymerase interaction machineries with sufficient diversity to promote or inhibit DNA transcription by RNA polymerase. What remains largely elusive, however, is how the machinery is turning.
The structure of this review is relatively straightforward. The various known regulatory families are treated individually, as far as possible with examples of catabolic pathways. Specific attention has been given to describing the genetic organization of the regulatory genes, promoters, and target operon(s); this is followed by a discussion integrating the knowledge of signaling molecules, DNA binding properties and operator characteristics, regulator-DNA structure, and evidence from regulatory mutants to arrive at a possible mechanism of transcription activation. What is not specifically treated in this review is how regulatory systems themselves are embedded in the host's physiology and controlled by other global regulatory systems. For information about these aspects, readers are referred to other specific overviews, such as references 23, 232, and 265. For sake of the overview, we have refrained from too many in-depth details of very specific individual transcription regulators.

LysR FAMILY OF TRANSCRIPTIONAL REGULATORS
Catabolic Operons Controlled by LysR-Type Regulators
LysR-type transcriptional regulators (LTTRs) comprise the largest
family of prokaryotic regulatory proteins identified so far
(
84,
224). The family has expanded to over 100 members that
have been identified in diverse bacterial genera. This diversity
is also reflected in LTTRs associated with degradation pathways
of aromatic compounds (Table
1) (
44). A large group of LTTRs
regulates a single target operon only, such as CatR controlling
catBCA expression for catechol metabolism in
Pseudomonas putida (
215), ClcR controlling the
clcABDE operon of plasmid pAC27
(
33), TcbR controlling the
tcbCDEF operon in plasmid pP51 of
Pseudomonas sp. strain P51 (
263), and CbnR controlling the
cbnABCD operon for chlorocatechol metabolism in
Ralstonia eutropha (
163).
TfdR (and/or its identical twin TfdS) also regulate an operon
coding for chlorocatechol metabolism (i.e., the
tfdDCEFB genes),
but the same regulators also control the expression of two other
operons,
tfdA and
tfdDIICIIEIIFIIBIIK, all of which are involved
in degradation of 2,4-dichlorophenoxyacetate in
R. eutropha JMP134 (and are located on plasmid pJP4 [Fig.
1A ]) (
127). Similarly,
CatR of
P. putida can coregulate the expression of the
pheBA operon for phenol degradation and of the
catBCA genes when this
operon is provided on an additional plasmid (
104). Like TfdR
and TfdS, the NahR protein is a master regulator for the regulon
of naphthalene degradation and acts by controlling expression
from both the
nah operon, required for the metabolism of naphthalene
to salicylate and pyruvate, and the
sal operon, encoding the
enzymes for salicylate conversion (
225,
228,
274). In this case,
both operons are present on the NAH7 plasmid. Two LTTRs have
been implicated in the transcriptional control of benzoate degradation
in
Acinetobacter sp. strain ADP1. In this microbe, BenM regulates
expression from the
benABCDE and
benPK operons, which encode
the enzymes for conversion of benzoate to catechol. CatM also
regulates expression from
benPK but in addition regulates expression
from the
catBCIJFD operon, leading to further metabolism of
cis,
cis-muconate to the tricarboxylic acid cycle (Fig.
1B).
The
catA gene, encoding catechol 1,2-dioxygenase, which converts
catechol to
cis,
cis-muconate, is not present in the two operons
but is also regulated by both CatM and BenM (
34,
212). CatM
and BenM also interfere with expression of the
pobA gene for
4-hydroxybenzoate metabolism, perhaps by preventing the expression
of the
pcaK uptake system (
16). Although LTTRs are often associated
with
ortho-cleavage pathways of catechol, they are also involved
in a large variety of other degradation pathways (Table
1).
For example, NtdR controls the genes encoding nitroarene dioxygenase
in
Acidovorax sp. strain JS42 (
125); the TsaR protein controls
the expression of the
tsaMBCD genes, which encode the first
steps in the degradation of
p-toluenesulfonate in
Comamonas testosteroni T-2 (
253); and BphR2 is involved in the regulation
of a biphenyl catabolic gene cluster of
Pseudomonas pseudoalcaligenes KF707 (
268). Preliminary data for regulation of the biphenyl
pathway indicate that BphR2 is activating the expression of
a first operon [
bphA1A2(orf3)A3A4] whereas a second regulatory
gene (
bphR1, a regulator of the GntR family) is activating the
expression of the second operon (
bphX1X2X3D). LTTRs have also
been identified in

-hexachlorocyclohexane degradation in
Sphingomonas paucimobilis (
148), in aniline degradation in
P. putida (
67),
and in catabolism of 3-phenylpropionic acid in
Escherichia coli K-12 (
42). A longer list of LTTRs involved in transcriptional
control of aromatic compound degradation is presented in reference
44.
View this table:
[in this window]
[in a new window]
|
TABLE 1. Regulatory proteins from the LysR family involved in expression control of pathways for degradation of aromatic compounds
|
In general, the gene for LTTRs lies upstream of its target-regulated
gene cluster and is transcribed in the opposite direction (Fig.
1A and B), but exceptions to this rule exist. For example, the
gene for the SalR regulator in
Acinetobacter sp. strain ADP1
is present within the transcriptional unit
salRA. The
salA gene
is coding for salicylate hydroxylase, which converts salicylate
to catechol. Experimental evidence suggests that SalR is regulating
the expression of itself and of
salA (
101). The
phnS gene (coding
for a further uncharacterized LTTR) is cotranscribed as the
first gene of an operon including the
phnFECDAL catabolic genes
for naphthalene and phenanthrene degradation in
Burkholderia sp. strain RP007 (
119).
All identified LTTRs involved in aromatic degradation pathways act as transcriptional activators for their target metabolic operons in the presence of a chemical inducer, which is usually a pathway intermediate (33, 128, 212, 215, 227). In some cases, the effectors are (substituted) muconates which have lost their aromatic character, whereas in other systems aromatic compounds act as effectors (e.g., salicylate, catechol, and nitrotoluene [Table 1]). There is also experimental evidence for competition of several compounds on the regulatory protein. For example, fumarate reversibly inhibits the formation of the clcA transcript in in vitro transcription assays in the presence of purified ClcR and 2-chloro-cis,cis-muconate (138). The presence of cis,cis-muconate decreases the affinity of the BenM protein for benzoate (31). All LTTRs repress their own expression, and both autorepression and activation of the catabolic operon promoter are exerted from the same binding site, which is called the regulator or repressor binding site (RBS) (20, 216, 227). Autorepression was not influenced by the presence of an inducer in the case of BenM (20), but expression of the clcR and tcbR promoters was slightly enhanced in the presence of an inducer (33, 263). Relatively few data exist on autorepression mechanisms, since most studies on LTTRs have focused on the mechanisms of target gene activation.
Structure and Conformation
LTTRs involved in the degradation of aromatic compounds are
composed of 394 to 403 amino acid residues with a molecular
mass of between 32 and 37 kDa. All the evidence presented so
far points to tetramers being the active form of LTTRs. ClcR
and CatR have been identified as dimers in solution (
32,
181),
but two dimers are needed to bind DNA (
141). CatM, BenM, and
CbnR were found to form tetramers (
20,
30,
155), and NahR probably
also acts as a tetrameric form (
226). The well-studied LTTR
CysB, which is not involved in the activation of pathways for
aromatic-compound degradation, also forms tetramers in solution
(
88,
145). Only TsaR remains as monomer in solution (
253). LTTRs
have a conserved domain organization, which has been determined
from mutagenesis studies and sequence alignments (
224). A DNA
binding region with a predicted helix-turn-helix (HTH) motif
is located in the 66 N-terminal amino acid residues of the protein,
two regions located between residues 95 to 173 and residues
196 to 206 are involved in inducer recognition, and one region
between residues 227 and 253 is supposed to be involved in multimerization
(Fig.
2A).
Recently, the first complete LTTR has been crystallized (CbnR)
(
155). Crystals of BenM and CatM devoid of their N-terminal
DNA binding domain have also been obtained, but their structures
have not been resolved yet (
29). CbnR crystallized as a tetramer
(Fig.
3) with two main parts, the four DNA binding domains (residues
1 to 58) and a central body (
155). The four DNA binding domains
have no interactions with each other, whereas the central body
of the tetramer is composed of four intertwined regulatory domains
(residues 88 to 294 of each subunit). The tetramer structure
can be regarded as a dimer of a dimer, whereby each dimer is
composed of two subunits in different configurations. The two
subunits in each dimer are connected through the coiled-coil
linker (residues 59 to 87), which at the same time separates
the DNA binding domain and the central body (Fig.
3). Subunit
A of the AB dimer interacts with the regulatory domains of both
subunits Q and P of the other (PQ) dimer, whereas subunit B
interacts only with P (Fig.
3). The structure seems to allow
easy transmission of conformational changes, for example in
the central body, the DNA binding domains. The DNA binding motifs
in the tetramer are presented in such a way as to form a V-shaped
structure, which matches exactly with the distance and configuration
of the two DNA binding sites (Fig.
3). Although the mode of
action and the location of the effector binding pockets still
need better definition, this structural model beautifully fits
and explains previous experimental evidence with the LTTRs.
Mechanisms of Activation
Due to their tetrameric form, LTTRs interact with several sites
on the DNA of the promoter region. Classically, DNA interactions
are shown by DNase I footprinting techniques and purified regulatory
protein. Interestingly, DNase I cleavage patterns of the protein-bound
nucleotide regions were similar for ClcR, CatR, TcbR, CbnR,
and, to a lesser extent, NahR. The different interactions are
explained in more detail for ClcR. ClcR binds the
clcA promoter
irrespective of the presence of inducer (
32,
141,
182). However,
in the absence of inducer, ClcR protects a 27-bp region (RBS)
from 79 to 53 and a 10-bp region (activator binding
site [ABS]) from 37 to 28 relative to the transcription
start site. Each region is supposed to be bound by one of the
two dimers in the tetramer (Fig.
4). The RBS contains an interrupted
inverted repeat, ATAC-N
7-GTAT, with the consensus LTTR binding
motif T-N
11-A (
224). Two hypersensitive bands (52/51
and 42) also show up on ClcR-bound promoter DNaseI footprints.
This may reflect the bending imposed on the DNA by the V-shaped
configuration of the tetramer (Fig.
3). In the presence of inducer,
the hypersensitive band at 42 disappeared and occupation
of the ABS shifted from 37 to 41 (
141), suggesting
that the bending angle is relaxed on interaction with the effector.
Conformational changes on effector binding could be detected
for benzoate and
cis,
cis-muconate binding to BenM (
31). Measurements
of the bending angle of the
clcA promoter in the absence (71°)
and in the presence (55°) of effector corroborate this idea
of bending relaxation (
140). Similar bending angles were reported
for CbnR at the
cbnA promoter in the absence and presence of
inducer, although for CbnR no changes in DNase I footprints
were observed as for ClcR (
163). The role of the RBS and ABS
is not completely clarified. Although ClcR and CbnR contacted
both the RBS and ABS in the absence of inducer, CatR did not
(
215,
216). It was concluded that the regulatory proteins have
a higher binding affinity to the RBS than to the ABS, since
a fragment with only the ABS is not bound by ClcR or CatR (
139,
181). However, contacts to the ABS are supposed to be necessary
for mediating interactions with RNA polymerase (RNAP), and fragments
with only the RBS do not lead to in vitro transcript production
in the presence of ClcR, RNAP, and inducer (
139).
Further contacts seem to occur between the regulatory protein
complex and the C-terminal domain of the

-subunit (

-CTD) of
RNAP. This was concluded from the lack of mRNA synthesis in
in vitro transcription experiments with CatR (or ClcR), the
catB (
clcA) promoter,
cis,
cis-muconate, and RNAP devoid of the

-CTD (
28,
139). A direct interaction of NahR with the

-CTD of
RNAP has been demonstrated by using a yeast two-hybrid system
(
178), and this interaction was not influenced by the presence
of salicylate. Chugani et al. (
28) postulated that the regulatory
complex was directing the

-CTD of RNAP to a region between the
RBS and the ABS, which they called the UP-motif (Fig.
4). Interaction
with the UP-motif would increase the affinity of RNAP to the
promoter (
28). However, exactly how this process would lead
to transcription activation is not known. The degree of DNA
supercoiling has also been implicated in controlling the level
of transcription activation from LTTR-dependent promoters. This
has been concluded from in vitro transcription experiments with
CatR, in which supercoiled templates produced no mRNA transcript
except in the presence of
cis,
cis-muconate whereas linearized
templates did (
28). Perhaps the regulatory protein can overcome
the torsional constraint on the DNA in the presence of inducer,
thereby facilitating open-complex formation by RNAP.
In some cases, a third DNA binding site further downstream of the transcriptional start site has been identified. For example, CatR binds with low affinity to a region between +162 and +196 of the catB gene (27). This site has been named the inhibitor binding site (IBS) and is supposed to prevent excessively high expression from the catBCA operon by titrating CatR protein. The affinity of binding of CatR to the IBS increased at higher inducer concentrations, and catB promoter fragments containing the IBS had a three- to fourfold lower expression than those without IBS (27). IBS regions have also been identified in the pheBA operon and clcABD operon (27).
BenM has the unique peculiarity (for the moment) that the inducers benzoate and cis,cis-muconate can have synergistic effects on the activation process compared to the effects of each inducer alone (20, 31, 34). In addition, BenM represses benA transcription in the absence of inducer. Benzoate and cis,cis-muconate alone had very different effects on the patterns observed in DNase I footprints of BenM on the benA promoter than did both inducers simultaneously. In the absence of inducer, BenM bound two areas with dyad symmetry, site 1 (ATAC-N7-GTAT) at positions 57 to 71 and site 3 (ATTC-N7-GTAT) at positions 5 to 19. Several hypersensitive sites were detected (at positions 50, 45, 39, 36, 34, 29, and 24), suggesting again a clear bending of the DNA imposed by the BenM regulatory complex. In the presence of cis,cis-muconate or benzoate, BenM still protected site 1 but no longer protected site 3. When both inducers were present simultaneously, the number of hypersensitive sites was reduced and instead a region called site 2 (which also contained a dyad symmetry motif, ATAC-N7-GTGT, located between 36 and 50) was protected from DNase I cleavage (20). The authors hypothesized that BenM binding to site 3 (which overlaps with the 10 region) causes the observed repressive effect in the absence of inducer. In the presence of inducer, is BenM released from site 3, enabling RNAP to access the promoter, whereas BenM binding to site 2 would lead to more productive contacts to RNAP and a higher transcriptional output.

IclR FAMILY OF TRANSCRIPTIONAL REGULATORS
Catabolic Operons Controlled by IclR Regulators
IclR-type regulators have a similar structure as the LysR-type
regulators (
224), but rather dissimilar amino acid sequences
distinguish the two families. IclR-type regulators are generally
transcriptional repressors (
86,
132,
156,
245); however, those
which control catabolic pathways have all been described as
activators (Table
2). For example, PcaU of
Acinetobacter sp.
strain ADP1 (
75), PcaR of
P. putida (
213), PcaR of
Agrobacterium tumefaciens, and CatR and PcaR of
Rhodococcus opacus 1CP (
58,
59) are activators for the
ortho-cleavage pathways which they
regulate. However, in the absence of inducer they may still
act as repressors, as was shown for PcaU (
254). Further IclR
members are MhpR, which activates the
meta-cleavage pathway
in 3-(3-hydroxyphenyl)propionic acid degradation by
E. coli (
61); PobR, which is the activator for the 4-hydroxybenzoate
degradation pathway in
Acinetobacter sp. strain ADP1 (
45), and
OhbR, controlling the genes for the oxygenolytic
ortho dehalogenation
of halobenzoates (
256).
In general, the gene for the IclR-type regulator lies upstream
of its target gene cluster and is transcribed in the opposite
direction (Fig.
1C). An exception is the
pcaR gene of
P. putida (
160). PcaR actually controls four distinct gene clusters required
for the degradation of protocatechuate to tricarboxylic acid
cycle intermediates and of the 4-hydroxybenzoate transporter
PcaK (
160). The
pcaR gene lies upstream of
pcaK and is transcribed
in the same direction (
90,
159,
213). PcaR from
P. putida and
PobR and PcaU from
Acinetobacter sp. strain ADP1 repress their
own expression (
46,
81,
254). It is thought that the mechanism
of autorepression is different among IclR-type regulators, since
not all of them bind at the same position on the promoter region
(
75,
81,
213) and since for some of them the addition of effectors
changes the expression of the regulatory gene itself. For example,
expression of
pcaR and
pobR is independent of the usual effectors
for PcaR and PobR (
46,
81) but
pcaU expression increases in
the presence of effectors for PcaU (
75).
Structure and Conformation
The size of IclR-type regulators is around 238 to 280 amino
acid residues (25 to 30 kDa) (
59,
61,
82,
112,
256). IclR-family
members have an HTH DNA binding motif in the N-terminal domain
(
45,
61) and a C-terminal domain involved in subunit multimerization
and effector binding (
112). This was confirmed by the crystal
structure of IclR from
Thermotoga maritima 0065 (Fig.
5) (
275),
which showed that the amino acid residues previously identified
to be involved in PobR inducer specificity (
112) are present
in IclR and comprise a pocket in the C-terminal domain (
275).
Although PcaU and PcaR from
P. putida formed dimers in solution
(
81,
193), IclR crystallized as a dimer of a dimer with an asymmetric
configuration (
275). The two subunits within one IclR dimer
interact solely at the interface of their DNA binding domains.
As a consequence, the distance between the HTH motifs within
one dimer is relatively short and results in a structure favorable
for binding relatively short (12- to 14-bp) palindromic DNA
sequences with specific contacts predominantly in the major
groove of the DNA. The C-terminal domains do not contact each
other in the dimer, but they do bridge with the C-terminal domains
from the neighboring dimer, which is oriented in asymmetric
fashion (Fig.
5). It is not really clear how the tetramer interacts
with the DNA. Mass spectrometric data revealed that four IclR
subunits are present per DNA containing one single palindrome
(see below). The presumed ligand binding region is close to
the region involved in tetramerization, suggesting that ligand
binding and tetramerization may be linked. Moreover, the tetramer
seems to be the active DNA binding form since, in mass spectrometric
studies, four IclR subunits bound one synthetic DNA containing
one single palindrome. The stoichiometry of two protein subunits
for one DNA molecule was never detected (
48).
Mechanism of Transcription Activation
There is no clear consensus on the binding site for IclR members
(Table
2). For example, the MhpR binding site is formed by one
15-bp palindrome that lies 50 to 66 nucleotides upstream of
the
mhpA transcription start site (
252), but those of PcaU and
PobR are three perfect 10-bp sequence repetitions that lie between
53 and 94 bp upstream of the
pobA and
pcaI transcription start
sites, respectively (
46,
75,
193). Two of the 10-bp sequence
repetitions form one palindrome, and the third repeat is oriented
opposite to the second one but separated by another 10 bp (
193).
In contrast to those, the PcaR binding site is formed by a series
of 15 nucleotides present twice in the
pcaI promoter and overlapping
with the 10/35 promoter region (
81). One might
thus conclude that when the regulators conform to their binding
sites, they must be different between MhpR, PobR, PcaU, and
PcaR.
IclR-type regulators bind their promoter DNA in the absence of effector, and adding effector molecules had no effect on the affinity of the protein-DNA interactions displayed by purified PobR, PcaU, PcaR, and MhpR (46, 75, 81, 252). When, however, the chemical effector was added to a mixture of regulator (in this case PcaR), purified
70-RNAP, and a pcaI promoter fragment, the formation of a PcaR-RNAP-DNA complex was enhanced compared to the situation without effector (81). The authors suggested that the role of the regulatory protein might be to favor the recruitment of RNAP to the promoter, perhaps by optimizing the critical distance between the 35 and 10 elements in the pcaI promoter from 16 to 17 bp (81). The same effect of enhanced complex formation was also found for SoxR and MerR (6, 85). Also, in the mhpA promoter the 35 and 10 elements are separated by 16 bp (252). However, the pobA promoter (regulated by PobR) already has a spacing of 17 bp (75), and thus the generality of this promoter distance optimization as an activation mechanism for IclR-type regulators is debatable.

AraC/XylS FAMILY
Catabolic Operons Controlled by AraC/XylS-Type Regulators
For years the XylS protein was the only member of the AraC family
which was involved in expression control of a catabolic operon,
namely, the
meta-cleavage pathway operon for degradation of
meta-toluate located on the TOL plasmid in
P. putida (
92). Recent
alignment studies have shown that more than 300 proteins, some
of which may be involved in the control of catabolic pathways,
contained a typical stretch in the C-terminal part of about
100 amino acids that would classify them as AraC/XylS-type regulators
(
251). The remaining part of the proteins can be very different,
though (see below). AraC/XylS-type regulators for catabolic
operons generally act as transcription activators in the presence
of a chemical effector molecule (Table
3). Some of the more
recently discovered catabolic gene regulators of the AraC/XylS
family are PobC of
P. putida WCS358 (
13), PobR of
Azotobacter chroococcum (
198), and PobR of
Pseudomonas sp. strain HR199
(
173). PobC and PobR regulate the expression of a
pobA gene
for
p-hydroxybenzoate hydroxylase. HpaA is a XylS-type protein
found in
E. coli and regulates the expression of the
hpaCB genes
for
p-hydroxyphenylacetate hydroxylase (
195). Other family members
identified in degradation pathways are CbdS, controlling the
2-halobenzoate dioxygenase genes in
Burkholderia sp. strain
TH2 (
246); BenR, controlling the benzoate 1,2-dioxygenase operon
in
P. putida (
36); CadR, controlling the genes for 2,4-dichlorophenoxyacetic
acid degradation in
Bradyrhizobium sp. strain HW13 (
109); and
IpbR, which regulates the expression of isopropylbenzene degradation
in
P. putida RE204 (
51).
View this table:
[in this window]
[in a new window]
|
TABLE 3. Major AraC/XylS-type regulators controlling the expression of degradation pathways for aromatic compounds
|
Most of the genes for XylS-type regulators lie upstream of their
target operon, but, in contrast to
lysR-type genes, they are
transcribed in the same direction as the target genes. For example,
cbdS,
hpaA,
cadR,
benR, and
phcT are all transcribed in the
same direction as the genes they are regulating (
36,
109,
196,
246). The
pobR and
pobC genes, on the other hand, are transcribed
in the opposite direction (
13,
173,
198). The
xylS gene itself
is also transcribed in the opposite direction to the
meta-cleavage
pathway operon (Fig.
1E) but is located downstream of it (
93).
Expression of the genes for XylS-type regulators is not controlled just by themselves but in many cases by other activators or cascades. The best-studied example is XylS. Expression of xylS is strongly dependent on another regulatory protein XylR (see further below). XylR stimulates xylS-transcription from a
54-dependent promoter (called Ps1) when cells are grown on xylenes (69, 134). In the absence of suitable aromatic inducers, the xylS gene is expressed at low constitutive levels from a
70-dependent promoter called Ps2 (69). The hpaA regulatory gene has the unusual feature of being cotranscribed with the hpaX gene, which lies directly upstream of hpaA (194, 195). Expression of hpaA takes place from two promoters, one located directly upstream in the coding region of hpaX and the second located upstream of hpaX, in which case a bicistronic transcript is produced (195). Another example is provided by the phcT regulatory gene. PhcT is at the top of a regulatory cascade controlling phenol degradation (250). PhcT enhances transcriptional activation of the phc operon for phenol degradation by interacting with another regulator, PhcR, but at the same time it represses expression of the phcR gene itself. The dual action of PhcT is possible because its binding site is located in the intergenic region between phcR and the phc phenol operon, which themselves are oriented divergently (250).
Structure and Conformation
XylS/AraC-type regulators involved in degradation control of
aromatic compounds are typically between 293 and 322 amino acids
in size, with a molecular mass around 35 kDa. One exception
is PhcT, which has only 257 amino acid residues with a predicted
molecular mass of 28 kDa. As far as has been determined, most
AraC members form dimers in solution (
21,
24). The solution
state of XylS has not been determined directly, since the protein
is very difficult to purify. Ruiz et al. found that a peptide
containing only the N-terminal end of XylS was able to dimerize
(
217). The C-terminal end of XylS/AraC-type regulators is the
most highly conserved part among this protein family and contains
two HTH motifs within a region of 100 or so amino acid residues
(Fig.
2C) (
71). In XylS the two HTH motifs comprise residues
231 to 252 and 282 to 305 (
133), and a truncated XylS polypeptide
with only the 112 C-terminal residues was capable of binding
and activating transcription from the P
m promoter (
103). Two
AraC family members (i.e., Rob and MarA) have recently been
crystallized (
114,
210) (Fig.
6), but they do not match the
most common AraC architecture, since MarA is a single-domain
protein (with only a DNA binding domain) and Rob has the DNA
binding domain located at the N terminus of the protein (
52).
MarA and Rob were crystallized as one monomer bound to a DNA
fragment containing one binding site, CCAC-N
7-TAA and GCAC-N
7-CAA,
respectively (Fig.
6). The two HTH motifs of MarA bind to adjacent
segments of the major groove, with the helical axes of the recognition
helices almost parallel to the DNA base pairs (Fig.
6). Because
the recognition helices in the HTH motifs protrude from the
same face of the protein, MarA binds to one face of the DNA.
The two HTH motifs are connected by a rigid central linker helix
that imposes their orientation and distance on the DNA binding
site. Binding results in a bending of the DNA at an angle of
35°, because the two recognition helices are separated by
27Å whereas the pitch of the DNA B-form is 34 Å
(
210). The structure of the Rob DNA binding domain is quite
similar to that of MarA, but two main differences were observed
in the protein-DNA complex (Fig.
6). First, the DNA was not
bent in the structure obtained with Rob, and second, only one
protein helix was contacting the major groove of the DNA (
114).
In addition, nonspecifically attached Rob subunits were present
in the crystallographic structure on the other side of the target
DNA, which could be interpreted as an artifact (
114). Martin
and Rosner suggested that the presence of the second monomer
prevented bending of the DNA and hence interaction of the second
protein helix to the major groove of the DNA (
137). On the other
hand, it has been suggested that the Rob structure represents
the state required for transcription activation, since conserved
residues of one protein helix in the HTH-motif are not contacting
the DNA but are available for interactions with the transcriptional
machinery (
114). Gallegos et al. had already previously suggested
that conserved amino acids in this part of the HTH motif may
contact the transcriptional machinery whereas the first helix
would be more variable and involved in recognition of the target
promoter (
71).
The N-terminal end (also called the regulatory domain) of XylS/AraC
members is not well conserved. The N-terminal domain of AraC
has been crystallized in the absence and in the presence of
arabinose, but it has such a low percent identity to XylS (12.5%)
and XylS-mediated transcription activation from P
m is so different
from AraC and the P
BAD promoter (
52,
71) that extrapolation
of the AraC structure to XylS is doubtful. Structural ideas
were retrieved, however, from genetic evidence and different
XylS mutants. For example, single point mutations in the N-terminal
end of XylS resulted in proteins responsive to other aromatic
inducers, which suggests a role for the N-terminal end in effector
recognition (Fig.
2C) (
144,
218). Furthermore, some mutations
in this region impaired the in vitro formation of cross-linking
products between XylS peptides containing only the N-terminal
part fused to the maltose binding protein. This was interpreted
such that the N-terminal part of XylS would be involved in dimerization
as well (
217,
239). Both C- and N-terminal parts can act independently
(
218,
219). For example, mutations in both the C- and N-terminal
regions of XylS can yield semiconstitutive mutants (
203) or
suppressors (
143). This suggests there is some form of "cross
talking" between the two domains, but the mechanism of this
remains to be resolved.
Mechanisms of Activation
An understanding of the activation mechanisms by the "catabolic"
members of the XylS/AraC family may be biased by the relatively
large body of knowledge about XylS compared to others. A first
peculiarity of the XylS system is that activation can take place
in two modes, i.e., at low
xylS expression levels in the presence
of an inducer (
66,
204) and on overexpression in the absence
of inducer (
91,
94,
142,
202,
241), although the latter mechanism
may have no physiological meaning for the
xyl pathway. At least
BenR seems to behave similarly to XylS in this respect (
36).
XylS probably binds as two monomers or one dimer to two direct sequence repeats in the Pm promoter. This can be concluded from crystallographic data for the two AraC members Rob and MarA (114, 210). DNase I footprinting of the XylS interaction on the Pm promoter showed a protected region from nucleotides 78 to 28 upstream of the transcription start site (102, 103). The protein bound along one side of the DNA, covering four helices and thereby making specific contacts in four adjacent major grooves (102). By earlier site-directed mutagenesis studies, a consensus direct repeat (TGCA-N6-GGNTA), which is present twice in the Pm promoter between 35 and 49 and between 56 and 70, had been identified as the binding determinant (70, 78, 107). In the presence of m-toluate, the degree of protection by XylS on the Pm promoter increased (102, 103), suggesting that the affinity of XylS to its binding site had changed. Subsequent in vivo methylation studies showed an altered methylation protection pattern of the XylS-bound region in the presence of m-toluate, which indicates that conformational changes take place under inducing conditions (78).
Strangely, XylS-mediated transcription activation from the Pm promoter is independent of
70-RNAP (136) but during exponential growth is dependent on the alternative sigma factor
32, which normally is involved in the heat shock response (135). This has led to the suggestion that the presence of the chemical effector m-toluate is triggering a similar response for the cell to the heat shock response. In the late exponential and stationary phases, the sigma requirement for the Pm promoter changes to
38 (135, 136). However,
38-RNAP uses exactly the same promoter region in the Pm promoter as that used by
32 (136). Mutants can be obtained with mutations in the N-terminal domain of XylS which change the requirement of XylS for
38 to
70 (203).
A large number of XylS/AraC members, including XylS itself, seem to require contact with
-CTD and with parts of the
-factor in order to achieve full activation (15, 53, 116, 117, 131, 220). This was concluded mostly from in vitro transcription experiments and transcriptional reporter gene fusions with mutated RNAPs. A direct interaction between XylS and RNAP has not been demonstrated conclusively (251), but introducing 2 bp between the nucleotides at positions 36 and 37 of the Pm promoter abolished XylS-dependent transcription activation, probably because XylS and RNAP were offset and could no longer interact (77). In vivo dimethyl sulfate footprinting suggested that XylS can retain RNAP on the Pm promoter in the absence of inducer. In the presence of benzoate, RNAP was released, with concomitant transcription initiation (147).
What can be concluded about the role of XylS in the process of transcription activation? Apparently, XylS prevents open-complex formation in the absence of inducer but somehow recruits RNAP to bind to the Pm promoter. In the presence of inducer, XylS changes its own conformation and that of its binding site, which allows isomeratization of promoter-RNAP to form the open complex (251). Exactly how the effector mediates these changes and how this is transmitted to the DNA and RNAP remain elusive.

GntR-TYPE REGULATORS
Catabolic Operons Controlled by GntR-Type Regulators
Regulation by repression is rare for catabolic pathways. Ferrandez
et al. were the first to report that the product of the
paaX gene repressed the expression of two operons for phenylacetic
acid (PA) degradation (
paaABCDEFGHIJK and
paaZ [Fig.
1E]) in
E. coli strain W (
63). These operons code for an aerobic catabolic
pathway but have typical features of anaerobic degradation of
aromatic compounds, because of activation of PA to phenylacetyl-coenzymeA
(PA-CoA) by the action of a PA-CoA ligase (PaaK). By sequence
similarity, the
paaX gene product was classified as a GntR-type
repressor. The
paaX gene is located downstream of
paaK and is
transcribed in the same direction, although it is not part of
the same transcript (
63). Since then, a few other GntR members
have been found for catabolic pathways (Table
4). The repressors
PhcS and AphS regulate the expression of the phenol degradation
pathway in
C. testosteroni strains R5 and TA441 (
7,
249). The
phcS and
aphS genes both belong to a small operon (
phcRS and
aphRS), of which the second gene is coding for an NtrC/XylR-type
regulator (see below) (
7). The
aphRS and
phcRS operons are located
upstream of and transcribed in the opposite direction from their
target catabolic operons (
8,
249). The AphS protein acts as
a factor for silencing the
aph genes for phenol metabolism,
whereas AphR is its transcription activator. Knockout mutations
in the
aphS gene were shown to enhance the transcription of
the
aph structural genes and of the
aphR promoter as well (
7).
VanR, which represses the
vanAB vanillate demethylase genes
in
Acinetobacter, is also a GntR-type regulator (
149). The
vanR gene is transcribed in the opposite direction to and overlaps
with the
vanB gene. Transcriptional regulation of biphenyl degradation
in
Ralstonia eutropha A5 (
152),
Pseudomonas sp. strain KKS102
(
165), and
P. pseudoalcaligenes KF707, is now also assumed to
be mediated by GntR-type regulators (BphS) (
269). The
bphS gene
in
R. eutropha R5 is oriented in the opposite orientation to
the first gene of the biphenyl operon (
bphE) (
152). In the strain
KKS102,
bphS is separated from its target operon by an insertion
element (
165). The third regulatory gene (
orf0, now
bphR2) present
in a biphenyl catabolic regulon is also located upstream of
the target operon but transcribed in the same direction (
269).
The Orf0 (now BphR2) protein is atypical in the GntR group since
it is presumed to be an activator rather than a repressor.
GntR family members that control the degradation of aromatic
compounds (except Orf0) are transcriptional repressors in the
absence of the pathway substrates. In the presence of the pathway
substrate, repression is released by interaction of the regulator
with the aromatic compounds or one of its metabolites (
62,
149,
165,
249). This was interpreted as a loss of DNA binding affinity
mediated by the chemical inducer (see below) (
62,
165). The
mechanism by which Orf0 activates transcription is not known.
Strong evidence for its activator function comes from gel shift
assays performed with the
orf0 promoter region and purified
Orf0. In these experiments, OrfO bound the promoter fragment
more strongly in the presence of inducers (2,3-dihydroxybiphenyl
and 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate) than in their
absence (
269).
Structure and Conformation
GntR-like regulators are between 239 and 254 amino acids long
with a molecular mass of around 27 kDa. The PaaX protein is
considerable bigger, with 316 amino acids and a molecular mass
of 35 kDa. Structural information comes from GntR-type regulators
that are not involved in pathways for degradation of aromatic
compounds. Haydon and Guest first described bacterial regulators
of the GntR family as having similar N-terminal DNA binding
domains but displaying high heterogeneity among the various
C-terminal effector binding and oligomerization domains (Fig.
2D) (
83). This view has been largely confirmed by crystallographic
structure determination and mutagenesis studies (
199,
200,
259,
273). Exemplary for the GntR-type structure is FadR (
211), whose
structure has been resolved in the presence of its target DNA
and its cognate inducer (Fig.
7). FadR exists as a homodimer
in solution and binds DNA as a dimer (
199,
259,
260,
273). The
protein in the crystal structure showed an

/ß N-terminal
domain (residues 1 to 72) with the HTH motif and a C-terminal
domain (residues 79 to 228) that is formed by seven

-helices
with short connecting loops. The seven

-helices are packed together
to form a bundle, and a large cavity within this bundle makes
up the effector (myristoyl-CoA) binding pocket (
259,
260). N-
and C-terminal domains interact only via a short linker region
comprising two short

-helices. The two monomers in the dimer
are packed together in parallel fashion, resulting in reciprocal
interactions of the domains and linker regions across the interface
(
273). Only the tip of the paired

-recognition helices projects
orthogonally into the same major groove (
259,
273). Each terminal
portion of the

-recognition helix interacts in an identical
fashion with the DNA. Part of the HTH motif also penetrates
the minor groove of the DNA helix to make specific contacts
with two bases (
259). The DNA has a B-form conformation with
a curvature of 20° toward the protein, and this results
in a contraction of the central major groove and an expansion
of the opposite minor groove (
273).
Mechanisms of Regulation
The repression mechanism of GntR-type regulators seems to be
a simple hindrance for RNAP binding or open-complex formation
(Fig.
8). GntR-type proteins bind either the promoter region
itself or between the transcription and translation start sites.
For example, four regions on the
bphE promoter were bound by
purified BphS of
Pseudomonas sp. strain KKS102. The binding
sites are located between positions 12 and +3 (called
BS
I), +6 and +23 (BS
II), +27 and +40 (BS
III), and +44 and +58
(BS
IV) compared to the transcription start site. BphS has more
affinity to BS
I and BS
II than to BS
III and BS
IV, a difference
which was explained by the presence of inverted repeats in BS
I and BS
II (Table
4), and no such features in BS
III and BS
IV.
In fact, fragments with only BS
I and BS
II are sufficient for
BphS to mediate repression, whereas transcription from an artificial
promoter fragment containing only BS
III and BS
IV was not repressed
to a significant extent. Nevertheless, the strongest repression
was obtained when all four binding sites were present (
165).
BphS loses its ability to bind to the promoter in the presence
of the inducer 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid
(an intermediate in biphenyl metabolism).
A 15-bp imperfect palindromic sequence was identified in the
PaaX-dependent promoters
paaZ and
paaA. The palindrome was located
between positions 30 and 16 in the
paaZ promoter
and between +3 and +17 in the
paaA promoter. DNase I footprinting
showed that the PaaX protein actually protects a larger region,
which extends from 1 to +51 in the
paaA promoter and
from 30 to +17 in the
paaZ promoter (
62). Hypersensitive
sites were spaced at approximately 10-nucleotide intervals,
suggesting binding of PaaX to one side of the double helix.
The fact that PaaX protected the 10 box in the
paaZ promoter
but not in the
paaA promoter suggests a different mechanism
of PaaX repression in these two promoters (as shown in the model
in Fig.
8). In the presence of phenylacetate-CoA, binding of
PaaX to the
paaA and
paaZ promoters was released (
62). A sequence
of events leading to the release of repression can be deduced
from the FadR-DNA structure in the presence of myristoyl-CoA
(the inducer for FadR) (
259). Binding of the effector induces
conformational changes in the sensor kink helix

8 (Fig.
7),
which then forms two separate helices. As a result, some of
the side chains on this helix are pushed toward the neighboring
helix,

4 (linker region), which responds by shifting away from
helix

8 toward the N-terminal DNA binding domain. This shift
introduces additional contacts with the helix

1 in the N-terminal
domain, which tilts away and causes a hinge-bending motion of
both DNA binding domains of the dimer in opposite direction.
This leads to a change in the distance between the two recognitions
helices, which now lose their ability to interact with the DNA
helix (
259).

TetR-, MarR-, AND FNR-TYPE REGULATORS
TetR Family
Only one example of a TetR-type regulator involved in the regulation
of an catabolic pathway for aromatic compounds is known. This
protein, CymR, is a repressor for the expression of the genes
for
p-cymene (
cym) and
p-cumate (
cmt) degradation in
P. putida F1 (Fig.
1H; Table
5) (
50). The
cymR gene itself is positioned
upstream of and transcribed in the same direction as the
cym operon. Similar sequences have been identified in the
cmt and
cym promoter regions (Table
5) and may be the recognition sites
for the CymR repressor protein (
50,
164). CymR is supposed to
impose its repressing effect by inhibiting RNAP access to the
promoter. In the presence of the pathway effector,
p-cumate,
CymR is assumed to no longer bind to its operator site, in analogy
to the TetR repressor in the presence of tetracycline (
170).
Strangely,
p-cymene, the substrate for the
cym-encoded pathway,
is not an effector for CymR (
50). The CymR protein is 203 amino
acids long with a molecular mass of 23 kDa and is supposed to
form a dimer in solution, like the TetR protein, for which the
structure is known (
170). Its N-terminal part contains an HTH
motif (predicted for amino acids 19 to 64 in CymR), which is
responsible for DNA binding, whereas the C-terminal domain binds
tetracycline (
170). The C-terminal domains interact in the dimer
to form a core. The HTH motifs bind to the (palindromic) operator
sequence, with the recognition helices aligned parallel to the
major groove. The distance and the relative orientation of the
HTH motifs distinguish between the induced and the noninduced
status of TetR. Inducer binding triggers a sequence of

-helix
displacements, which results in an increasing separation of
the recognition helices. The shift of the recognition helices
along the major groove disrupts the contacts between the DNA
binding domains and the operator, causing dissociation of the
TetR operator complex (
170).
View this table:
[in this window]
[in a new window]
|
TABLE 5. TetR, MarR, and FNR family members and two-component regulators in degradation pathways of aromatic compounds
|
MarR-Type Regulators
The
nbz operon for aminophenol degradation on plasmid pNB1 in
P. putida HS12 is regulated by NbzR, a MarR-type repressor protein
(
176). The chemical inducer for the pathway has not been identified,
and it was proposed that another
trans-acting factor might be
involved in regulating pathway expression. Other MarR-type regulators
involved in catabolic pathways include HpcR (HpaR), the repressor
of the
hpc (
hpa) operon for 3- and 4-hydroxy- and 3,4-dihydroxyphenylacetic
acid (homoprotocatechuate) degradation in
E. coli strains C
(
214) and W (
68). In fact, current information from genome sequences
shows that the pathways for homoprotocatechuate degradation
are very common among
Gamma- and
Betaproteobacteria. CbaR, another
MarR-type regulator, controls the
cbaABC operon for 3-chlorobenzoate
degradation present on plasmid pBRC60 in
C. testosteroni BR60
(
197). 3-Chlorobenzoate and protocatechuate are effectors for
CbaR, leading to derepression (
197). The genes for benzoyl-CoA
reductase in
Rhodopseudomonas palustris are also under the control
of a MarR family member, named BadR. BadR activates rather than
represses gene expression (
55), although most other MarR family
members are repressors of gene transcription (
113,
171). Benzoate
is assumed to be the effector for BadR-mediated activation (
55).
Additional pathway control is exerted by the AadR regulator,
a FNR-type regulator, under anaerobic conditions (
55). The regulatory
genes
nbzR,
cbaR, and
hpcR are located upstream of and are transcribed
in the opposite direction to their target operons (
176,
194,
197).
badR is located upstream of and transcribed in the same
direction as its target operons but is separated from them by
one additional gene (
55). HcaR, the repressor of the hydroxycinnimate
(
hca) genes in
Acinetobacter sp. strain ADP1, is also a distant
member to MarR (28% identical aligned residues), which reacts
to a hydroxycinnamoyl-CoA thioester as an effector compound
(
180).
DNA binding studies have been performed with HpaR (68) and CbaR (197). CbaR contacts two sites (named BSI and BSII), which are located near the transcription start site. BSI is located approximately 40 nucleotides downstream of the transcription start site of cbaA, whereas BSII overlaps with it. An inverted repeat of 4 nucleotides separated by 6 and 9 nucleotides (GTTG-N6/9-CAAC) is present in the BSI region. Similar (but not perfect) inverted repeats are present in BSII (GTTG-N6-TAAC or GTAG-N9-TAAC), and it is presumed that CbaR interacts with the inverted-repeat sequences in some way. In DNase I footprinting experiments, CbaR bound to a BSI DNA fragment with higher affinity than to BSII, which led to the conclusion that independent CbaR proteins bind to each site. In the presence of 3-chlorobenzoate, benzoate, or protocatechuic acid, DNA binding by CbaR is disrupted, whereas 3-hydroxy- and 3-carboxybenzoate increased binding affinity by 60-fold. The physiological significance of this phenomenon is not understood (197). HpaR from E. coli is binding to two operator sites in the Pg promoter for the hpaGEDEFHI operon, one of which overlaps with the transcriptional start site (68). The operator around the transcriptional start site contains a perfect palindromic sequence (AATCATTAA-N4-TTAATGATT). Transcription from the Pg promoter is furthermore subject to strong catabolite repression by the cyclic AMP receptor protein.
Most MarR-type proteins carry a conserved HTH motif in the center of the protein, whose function would be to bind DNA (4). NbzR is atypical, since several conserved residues of the HTH motif are not present in NbzR. Instead, the protein possesses a putative leucine zipper motif (which is absent in other family members), which is thought to be responsible for the NbzR dimerization and DNA binding. Hence, Park and Kim suggested that the poor HTH motif of NbzR perhaps does not contribute to DNA binding (176). MarR-type regulators controlling catabolic operons are relatively small proteins. They contain between 148 and 196 amino acids and have a molecular mass of between 17 and 22 kDa. MarR has been crystallized (4, 130, 272). The structure revealed a MarR dimer with each subunit consisting of six helical regions. The N- and C-terminal regions encompassing residues 10 to 21 and 123 to 144, respectively, are closely juxtaposed and intertwine with the equivalent regions of the second subunit to form a domain that holds the dimer together (Fig. 9). These N- and C-terminal domains are linked to the remainder of the protein by two long antiparallel helices in each subunit. The helices lead to one globular domain, which includes residues 55 to 100 of each subunit and might be responsible for DNA binding. Although the globular DNA binding domains of the dimer are adjacent, they make minimal contact with each other. Four molecules of salicylate, which is an effector for MarR, were visible in the crystal structure: two at each subunit and two on either side of the proposed DNA binding helix (4).
FNR-Type Regulators
Three members of the FNR family of regulators were found to
be involved in controlling catabolic operon expression (Table
5). These include HbaR, which activates the expression of the
gene for 4-hydroxybenzoate-CoA ligase in response to 4-hydroxybenzoate
in
R. palustris (
56); AadR, also present in
R. palustris (
55);
and CprK of
Desulfitobacterium dehalogenans (
238). AadR is the
transcriptional activator for the
hbaR gene itself. It is also,
with BadR (see above), a coactivator for the
badD benzoyl-CoA
reductase gene in
R. palustris (
55,
56), functioning as an oxygen
sensor and enhancing the expression of the anaerobic degradation
pathway under oxygen exclusion. Upstream of the transcription
start sites of
hbaR and
badD, interrupted inverted repeats (TTGAT-N
4-ATCAA)
are found, which were postulated to be AadR binding sites (
55,
56). The
cprK gene is part of a cluster for
o-chlorophenol dehalogenase
(
238). One small transcript which encompasses the
cprBA genes
for the dehalogenase itself is induced under conditions of dehalorespiration;
the remainder of the
cpr genes are expressed constitutively.
At several points within the
cpr cluster, FNR-like binding motifs
were detected. Within the
cprB promoter, this motif (TTAAT-N
4-ACTA)
occurs at 41 nucleotides upstream of the transcription start
site and is presumed to be a CprK binding site (
238).
The proteins of the FNR family are generally between 233 and 242 amino acids in length with a calculated molecular mass of around 27 kDa. The best-characterized member of the family is FNR, a global regulator which represses the expression of genes involved in aerobic respiration and activates the expression of genes that permit the reduction of alternative electron acceptors under anoxic conditions. In its active DNA binding form, FNR is a homodimer containing one [4Fe-4S]2+ cluster per subunit (12). Integrity of the cluster is required for FNR dimerization, site-specific DNA binding, and transcription activation (108). The cluster is also essential for redox sensing by FNR. FNR is supposed to interact with the
-C-terminal domain and the sigma factor of the RNAP (121, 131). The amino acid sequence of AadR contains the essential conserved cysteine residues for iron-sulfur coordination and, as such, may be a redox sensor as well. In contrast, HbaR and CprK lack the characteristic N-terminal cysteines and are not specific sensors for anoxic conditions (56, 238).

TWO-COMPONENT REGULATORY SYSTEMS
Two-component signal transduction systems comprise the major
mechanisms by which bacteria sense environmental signals and
control global cellular processes. They typically consist of
two individual proteins, a sensory histidine kinase and a response
regulator. In the general model (reviewed in references
5,
54,
175,
209, and
243), signal perception by the N-terminal domain
of the sensor kinase catalyzes an ATP-dependent phosphorylation
of a conserved histidine in the central region of the protein.
Once the histidine is phosphorylated, the phosphoryl group is
transferred from the histidine to a conserved aspartate usually
found at the N terminus of the cognate response regulator. Phosphorylation
of the regulatory domain catalyzes the effector domain, which
is the final mediator for gene expression control. Although
this is a basic scheme, it is highly adaptable, and numerous
variations have been found.
Involvement in Regulation of Catabolic Pathways
A number of two-component regulatory systems are known to control
the expression of catabolic pathways. The first of these is
the TodST system, which was identified in
P. putida F1 and
P. putida DOT-T1 (
118,
151). TodST controls toluene degradation
from the
todX promoter, which lies upstream of the
todXFC1C2BADEGIH operon. The
todST genes are located downstream of but in the
same direction as
todH (Fig.
1I). The regulatory genes form
their own transcriptional unit. Expression from the
todX promoter
is elicited by growth on toluene (Table
5) (
118). In
P. mendocina,
the TmoST proteins regulate the expression of the
tmo toluene-4-monooxygenase
genes. The
tmoST genes themselves are not located in the direct
vicinity of the
tmo operon (
205). Another two-component system
regulates the expression of benzylsuccinate synthase in
Azoarcus sp. strain T and in
Thauera aromatica strain K172. Benzylsuccinate
synthase is the first enzyme in the anaerobic conversion of
toluene and is under the control of a two-component system named
TdiSR (
3,
126). In
T. aromatica strain T1, two potential two-component
systems,
tutC1B1 and
tutCB, seem to be involved in the regulatory
control of toluene degradation under aerobic and anaerobic conditions
(
35,
126). A further two-component system named BpdST was identified
as the possible sensor/regulator of the biphenyl degradation
pathway in
Rhodococcus sp. strain M5 (
115). As with the
todST genes,
bpdST is located downstream of the target operon. Transcription
activation by BpdST takes place in the presence of biphenyl
(
115). Finally, a two-component system called StyRS has been
described for the
styABCD degradation pathway of styrene to
phenylacetate (Table
5). StyRS-mediated expression from the
styA promoter is inducible by styrene but repressed by phenylacetate
(
166). StyRS analogs have been found in
Pseudomonas sp. strain
Y2 (
264), in
P putida CA-3 (
166), in
Pseudomonas sp. strain
VLB120 (
174), and in
P. fluorescens ST (
222). In all these bacteria,
the
stySR genes are located upstream of and in the same direction
as the
styABCD operon.
Structure and Conformation of the Sensor Kinase Component
The sensor kinase proteins of the two-component systems involved
in regulation of degradation pathways of aromatic compounds
are structurally dissimilar. One example is the TodS protein,
which is 978 amino acids long and has a molecular mass of 108
kDa. TodS has five predicted defined domains, of which the first
contained a so-called bZIP motif. The bZIP motif consists of
a stretch of several basic amino acid residues, which probably
contact DNA directly, and an adjacent region with a heptad repeat
of leucine residues (the leucine zipper) that mediates protein
dimerization (
74,
257). The presence of a bZIP domain in a sensory
histidine kinase was very unusual. The TodS bZIP domain alone
was shown to bind a DNA fragment upstream of the
todS start
codon. This region contained the sequence 5'-TGACTCA-3<29>', which
is identical to the recognition sequences of the eukaryotic
proteins FOS and Jun, which also contain the bZIP motif (
118).
The possible physiological relevance of the TodS bZIP binding
to the DNA is not known. The TodS protein also contains two
identical histidine kinase domains, called Hk1 and Hk2, spanning
amino acids 184 to 409 and 756 to 978, respectively. The histidines
at positions 190 and 760 are the sites of autophosphorylation.
The two domains also carry a peptide motif called the G1 and
G2 blocks, which are involved in ATP binding. An intrinsic response
regulator domain reminiscent of CheY (
266) spans amino acids
443 to 570 and could be potentially phosphorylated by other
signal-transducing proteins. Amino acids 34 to 153 contain a
hypothetical chemical sensor domain, whereas the region between
positions 592 and 735 is supposed to form the oxygen-sensing
domain (
26,
118). Oxygen-sensing domains are found in various
redox and light sensor proteins (
248,
276). The authors concluded
that TodS might actually be a dual sensor that is capable of
sensing both toluene as a primary signal and oxidative stress
in the cytoplasm (
118). Isolation of TodS effector specificity
mutants proved that the aromatic compounds directly interact
with the sensor kinase (
26). From amino acid similarity comparisons,
it was concluded that TutC, TmoS, and StyS are homologous to
TodS (
35,
205,
264).
In contrast to TodS, the TdiS protein of T. aromatica K172 is only 548 amino acids long and has a molecular mass of 63 kDa (126). TdiS has three distinct predicted domains. Two domains are found at the N terminus (residues 27 to 162 and 182 to 330); they are similar to each other and to other oxygen-sensing domains (see above). The C-terminal domain (residues 349 to 546) is a typical conserved histidine kinase domain. TdiS of Azoarcus sp. strain T and TutC1 of T. aromatica strain T1 are very similar in organization to TdiS. Leuthner and Heider suggested that the TdiS-type protein could be specific for anaerobic toluene metabolism whereas TodS (or StyS) would preferentially be involved in aerobic metabolism only (126). T. aromatica strain T1 can metabolize toluene under both aerobic and anaerobic conditions (60) and, interestingly, has two toluene sensor/response regulators, of which TutCB resembles TodST and TutC1B1 resembles TdiST. However, it is not known whether one of them really controls the aerobic pathway only and the other controls the anaerobic pathway.
The last type of sensory histidine kinase is found only in BpdS. BpdS is exceptionally long: 1576 amino acids with a molecular mass of 170 kDa (115). One region in the N terminus (residues 61 to 146) shows sequence similarity to a conserved domain of eukaryotic proteins, which use tyrosine or serine/threonine as acceptors of phosphoryl groups. Between residues 316 and 323, there is a Walker A motif that could bind ATP. The C terminus of BpdS contains the histidine kinase domain. In addition, seven potential hydrophobic transmembrane segments exist, which could mean that the C-terminal histidine kinase is located within the cytoplasm whereas the N-terminal part of the protein would stick in the periplasmic space. In this respect, BpdS resembles receptor or receptor-like kinase proteins, which carry out signal transduction processes in both plants and animals (115).
Structure and Conformation of the Response Regulators
Once the signals are perceived by the sensory kinases of the
system, the kinases transmit the signal in form of phosphorylation
to the response regulator. The response regulators (TodT, BpdT,
etc.) are 206 to 227 amino acids long and have a molecular mass
of between 23 and 25 kDa. The response regulators in the two-component
systems controlling the aromatic compound degradation pathway
have a very similar configuration. They contain an N-terminal
regulatory domain (residues 10 to 115 in TodT) with an aspartate
phosphorylation site and a C-terminal DNA binding domain (residues
144 to 187) with an HTH motif (
118). TodT binds the
todX promoter
even in the absence of phosphorylation (
118). The TodT binding
site (the tod box) has been identified as a 12-bp inverted repeat
with a 4-bp spacing (ATAAAC-N
4-GTTTAT) centered at bp 105.5
from the
todX transcriptional start site. The dyad symmetry
of the binding sites suggests that TodT binds as a dimer (
118).
The response regulator StyR of the StyRS system was shown to bind an identical sequence motif to TodT (i.e., ATAAAC-N4-GTTTAT); however, in this case the motif was centered at bp 44.5 from the styA transcription start site (Table 5) (222). The nonphosphorylated form of StyR was shown to be a monomer, but on phosphorylation the two monomers join to form a dimer (124). This is also known to occur in other two-component regulatory systems (37, 64, 89, 129, 243). StyR in dimeric form has a 10-fold-higher affinity for the styA promoter than does the monomer (124), which could mean that dimerization of the response regulator is needed for efficient recruitment of the protein on the promoter and subsequent transcription activation. Interactions of TodT or StyR with RNAP have not been experimentally probed, and it cannot be concluded that the transcription activation mechanisms should be the same.

XylR/NtrC-TYPE TRANSCRIPTIONAL REGULATORS INVOLVED IN CATABOLIC PATHWAYS
In contrast to the above-described regulatory proteins, which
control transcription mediated by
70-RNAP (except for XylS),
XylR/NtrC-type regulators activate RNAP containing the alternative
sigma factor
54. The
54-RNAP holoenzyme forms a stable complex
with 12 and 24 promoters but is unable to start
transcription without further activation (
17,
192,
223). Isomerization
to the open complex is strongly stimulated by specific regulatory
proteins, generally known as prokaryotic enhancer binding proteins.
The best-characterized member is NtrC, and often the family
of prokaryotic enhancer binding proteins is referred to as the
NtrC family. NtrC-type regulators bind to DNA regions called
upstream activating sequences (UASs), which are usually located
more than 100 bp upstream from the
54-RNAP binding site (
18,
19,
79,
150,
208). Interactions between
54-RNAP bound to the
12/24 region and the regulatory protein associated
with the UASs are often facilitated by a bend in the intervening
DNA, which can be the result of integration host factor binding
(
190).
Catabolic Operons Controlled by XylR/DmpR Subclass Regulators
Regulation of aromatic-compound degradation is very often mediated
by NtrC-type regulators. The best-studied examples of those
are the XylR and the DmpR proteins from
P. putida (see below).
For this reason, the specific subclass of NtrC-type regulatory
proteins which act on promoters from catabolic pathways is also
often referred to as the XylR/DmpR subclass, and we refer to
them as such here as well. Briefly, XylR from
P. putida mt-2
is one of the two main regulatory proteins for the xylene and
toluene degradation pathway encoded on the TOL plasmid (the
other being XylS [see above]) (
201). XylR is responsive to chemical
effectors such as
m- and
p-xylene, which are the substrates
for what is called the upper pathway. XylR in combination with
54-RNAP triggers expression from the P
u promoter (in front of
the
xylU gene) and from the P
s promoter, driving expression
from
xylS as well (
2,
47,
91,
111,
202). The gene for XylR itself
is located downstream of the
meta-cleavage pathway operon and
of
xylS (Fig.
1E). In addition to being a transcriptional activator,
XylR represses its own expression. Under inducing conditions,
autorepression of
xylR increases (
14,
134). The reason for the
autorepression seems to lie in the fact that the
xylR promoter
and the XylR binding sites in the intergenic regions for
xylS and
xylR overlap, which may prevent
70-RNAP binding to the
xylR promoter.
The other very extensively studied NtrC-type transcriptional regulator involved in the degradation of aromatic compounds is DmpR. DmpR regulates expression from the Po promoter, which drives transcription from one single large operon for phenol degradation (dmpKLMNOPQBCDEFGHI) that is present on the pVI150 plasmid in Pseudomonas sp. strain CF600 (234). The dmpR gene itself is located directly upstream of and is divergently oriented from dmpK. A large number of highly similar regulators to DmpR have been found, which all control phenol degradation operons (Table 6) (8, 153, 158, 177, 229, 249). A few other examples worth mentioning here are TbuT and TbmR, which control toluene monooxygenase gene expression in Burkholderia picketti PK01 (22) and Burkholderia sp. strain JS150 (98), respectively. Two other members are TouR, which controls the touABCDEF and dmp-like operons for toluene monooxygenase and phenol degradation in Pseudomonas stutzeri OX1 (10), and AreR, which is involved in the degradation pathway for aryl esters (areCBA) in Acinetobacter sp. strain ADP1 (100). The genes for TbuT and TouR are located downstream of the target operons tbuA1UBVA2C and touABCDEF, respectively, but are transcribed in the same direction (11, 22). Expression of tbuT is partly controlled by TbuT itself, since a transcript covering both the tbu structural genes and tbuT is synthesized in the presence of toluene, which starts at the TbuT-dependent promoter PtbuA1 (22). Also, areR is transcribed in the same direction as areCBA but is located upstream of it. Finally, HbpR is the regulatory protein which controls two small operons for 2-hydroxybiphenyl degradation (hbpCA and hbpD) in Pseudomonas azelaica HBP1 (97). The intergenic region between hbpR and hbpC looks as if it has been subject to recent duplication and deletion events, since a small 5' part of a second hbpR copy is still present (96). Expression from hbpR itself is autoregulated by HbpR, which could be attributed to a secondary set of HbpR binding sites overlapping the hbpR promoter (96).
The types of chemical effectors and cofactors required for XylR/DmpR-mediated
activation have been very well studied (Table
6). One of the
motivations for those studies has been the urge to modulate
the effector spectrum of the regulators by mutagenesis (
73,
237). XylR/DmpR-like activators require a chemical effector
and ATP as the cofactor. The effector is usually the primary
substrate of the target pathway or a compound related to this.
Both XylR and DmpR hydrolyze ATP or dATP, which is essential
for activation (
188,
270). In addition, XylR can hydrolyze GTP,
whereas DmpR only binds to but does not hydrolyze GTP, CTP,
and UTP (
270). Some aromatic compounds such as 2,4-dimethylphenol
and 4-ethylphenol can bind DmpR and activate ATP hydrolysis
without triggering transcription activation (unproductive effectors).
This process is not well understood but may involve a slightly
different conformational change required for ATP hydrolysis
and for productive contacts with the transcription machinery
exerted by productive and unproductive effectors (
168,
169).
Unproductive effectors can also act as competitive inhibitors
for productive effectors (i.e., those which lead to transcription
activation) (
168). 3-Nitrotoluene can also bind XylR without
mediating activation (
73,
221). In several cases, inducing compounds
which effect transcription activation are not direct substrates
for the target pathway, such as 2-aminobiphenyl and HbpR (
97).
Domain Organization
XylR/DmpR-type regulators are typically between 563 and 570
amino acids long (molecular mass of 62 to 68 kDa), with the
exception of AreR, which is 600 amino acids long. Since XylR
and DmpR have resisted full purification, there is no direct
structural information on those proteins, except ideas which
can be extrapolated from genetic experiments. We therefore use
structural data from other NtrC-type regulators, which are not
involved in the degradation of aromatic compounds, to illustrate
possible structural motifs for XylR/DmpR subclass members. Members
of the NtrC family in general display an ordered three-domain
structure, although the domains themselves are not necessarily
very similar among different regulators (
150) (Fig.
2E). The
C-terminal end (forming the so-called D-domain) contains the
HTH motif responsible for DNA binding (
162) and in some cases
for dimerization (
110,
184).
The central or C-domain is the most highly conserved region among NtrC family members, and seven highly conserved regions (C1 to C7) have been identified here (150, 172). Mutagenesis of the regions C1 (containing the Walker A motif), C4 (Walker B motif), and C7 in XylR and DmpR showed they are involved in ATP binding and hydrolysis (188, 270). Mutagenesis of and cross-linking experiments with DctD (an NtrC-type regulator not involved in catabolic pathways) showed the conserved C3 region to be interacting with RNAP through the ß and
54 subunits of the holoenzyme (106, 122, 267). In vitro interactions between
54 and PspF (a noncatabolic activator) took place between the I-region of
54 and the PspF C-domain, most probably involving the 6-amino-acid GAFTGA motif within the C3 region (25).
The so-called A-domain, which is located at the N-terminal end and is very specific for the different NtrC-type regulators, has been implicated in signal perception and hence determines the specificity of the protein (233). The A-domain of DmpR and XylR (211 amino acids long) was shown to interact directly with the inducing aromatic compounds, and various effector specificity mutations have been generated in this region of the protein (38, 73, 167, 168, 183, 221, 235, 236). One inducer binding site is present per monomer, which was demonstrated for DmpR (167) and which could be pinpointed to a subregion between amino acid residues 107 and 186 (237). A structural model of the XylR A-domain generated by a "fold recognition approach" (41) predicted eight
-helices and seven ß-strands connected by 14 loops. Based on this model and the different XylR/DmpR effector specificity mutants, five different regions in the A-domain were postulated to form the aromatic compound binding site. These are loops 12 (position 174), 10 (position 142), 4 (position 65), 2 (positions 37), and 14 (position 203). The A-domain was also shown to modulate the ATPase activity of the C-domain. This was concluded from observations that regulatory proteins with their A-domain deleted displayed constitutive ATPase activity and activated transcription to the same extent as the complete protein in the presence of an inducer (9, 185, 229, 236). Successive deletion of the A-domain identified a subregion between residues 160 to 210 which was sufficient to repress XylR-dependent transcription activity in the absence of the inducer (187). Several other lines of evidence (167, 185, 229) have led to the current hypothesis that the A-domain acts as movable domain which, in its closed state, represses the ATPase activity of the C-domain but, in an open state that occurs under inducer binding, exposes the constitutive ATPase activity. The connecting amino acid sequence between the A- and C-domains is provided by a short region called the B-linker, which seems essential for the change from the closed to the open state. DNA binding data with purified HbpR suggested that the protein assembles to the oligomeric form irrespective of the presence of the effector (255).
Structure and Configurations
Based on sequence similarities, NtrC-family members were classified
as members of the AAA+ superfamily (ATPases associated with
various cellular activities) (
157). Recent structural information
has confirmed this sequence-predicted classification. The structure
of the joined N-terminal regulatory and central ATPase domains
of NtrC1 (NtrC1
AC) from
Aquifex aeolicus and the structure of
the isolated central domain (NtrC1
C) were recently determined
in their ADP-bound form (Fig.
10) (
123). The central ATPase
domain in NtrC1
AC is inactive, whereas that of NtrC1
C is capable
of oligomer assembly, ATP hydrolysis, and transcriptional activation.
The resolution of these structures has been an important step
in recognizing the structural differences between the active
and inactive states of the central domain. NtrC1
AC is a dimer
in solution in which the regulatory domain of each monomer is
adjacent to the central domain of its partner in the dimer (Fig.
10A). This might also be the state for XylR/DmpR proteins, since,
for instance, DmpR without ATP, DNA, and inducer appeared as
a dimer in solution as well (
270). The main dimerization interface
is formed by the B-linker and monomers are held in a front-to-front
fashion in the dimer (Fig.
10A). The dimerization interface
seems important for maintaining the off-state of the ATPase
domain. In fact, mutations in the B-linker of XylR that disrupted
the linker's secondary structure resulted in a much higher background
expression of a single-copy chromosomal P
u::lacZ fusion (
72),
which seems in agreement with the presumed role of the B-linker.
The central domain protein NtrC1
C without the A-domain crystallized
as a ring-like heptamer (Fig.
10B). The ultrastructure of purified
PspF stabilized in oligomeric form with the ATP transition analogue
ADP-aluminium fluoride was reconstructed as a trimer of dimers
(or asymmetric hexamer) from cryoelectronmicrographs (
231).
The diameter and height of the NtrC1
C heptamer rings were approximately
124 and 40 Å, respectively, with a front-to-back packing
of the protomers. In this configuration, the ATPase domains
contact two others simultaneously on each side. In the NtrC
AC dimer, one side of the ATPase domain is contacting the other
subunit whereas the second one (ß-hairpin and GAFTGA
in Fig.
10) is interacting with the B-linker. Because of this,
an essential highly conserved Arg residue at position 293 is
far away from the bound ADP molecule in the dimer whereas in
the heptamer R293 comes close to the ADP of its neighboring
protomer. The Arg-293 residue could thus actually be contacting
the

-phosphate of ATP and could catalyze ATP hydrolysis in the
heptamer configuration. There is good evidence to assume that
XylR/DmpR-like proteins also form heptamers or hexamers as part
of their activation cycle. For example, addition of ATP

S and
the inducer 2-methylphenol resulted in mainly hexameric forms
of DmpR (
270). Although XylR has resisted purification attempts,
the effect of ATP

S and ATP on subunit oligomerization was detected
with purified XylR-

A (
186). Transmission electron microscopy
shows that XylR-

A and a P
u DNA fragment were forming larger
(XylR oligomers) and smaller (dimer) complexes, depending on
the presence of ATP (
72).
The GAFTGA-loop forms the motif that is assumed to be interacting with the RNA polymerase transcription machinery. In the NtrCC structure, all GAFTGA-loops pointed toward the middle central pore of the heptamer (Fig. 10B). This would create an extended binding surface for
54-RNAP, although it is not clear where exactly the A-domains would go in the heptamer. For the PspF transcriptional regulator (which, however, lacks an A-domain), the interaction surface to
54-RNAP was formed between the I-region of
54-RNAP and the GAFTGA-loop of PspF (25). The hexameric state observed for PspF (231) and the heptameric NtrCC structure strongly suggest that XylR/DmpR-type regulators form similar oligomeric complexes. However, very different from PspF and NtrC1, which do not have a specific effector domain, must be the mechanism leading to effector-mediated transcription activation. Garmendia and de Lorenzo have proposed an activation cycle for XylR (72). In the activation cycle, XylR would change between dimer (unbound) and heptamer/hexamer (bound to the DNA), with the disassembly process being triggered by ATP hydrolysis (Fig. 11). For XylR/DmpR-like proteins, which carry an A-domain, there must thus be some sort of mechanical movement of the A-domain in the oligomeric form on induction, probably mediated by the B-linker, thereby perhaps exposing the GAFTGA-motifs in the central part. However, the typical signature stretches of the B-linker are not present in recognizably similar form in some other XylR/DmpR-like proteins members such as HbpR and TbuT (169), which may indicate that the mechanistic "movement" is not a requirement per se or can be achieved by other structures than the B-linker only.
DNA Binding during the Activation Process
The current activation model does not include a specific function
for the DNA binding site occupied by the XylR/DmpR-subclass
regulatory proteins. Two functions have been proposed: (i) to
provide a "physical" support for the regulatory protein in the
vicinity of
54-RNAP and (ii) to aid in obtaining the active
form of the regulatory complex. This was concluded from experiments
in which the addition of the DNA fragment containing the binding
site increased the ATPase activity of XylR-

A or TouR (and TouR-

A)
(
9,
188). However, it has to be said that similar experiments
with DmpR showed a small or nonexistent stimulatory effect (
270).
XylR/DmpR-like proteins bind to an approximately 60-bp sequence which is located far upstream of the transcription initiation site (the UAS) (Table 6). This was shown from DNase I footprinting analysis for purified HbpR, as well as for DmpR and XylR variants devoid of their N-terminal A-domains (189, 247, 255). Interestingly, the protection patterns were quite similar for the three proteins, and matching DNA sequences forming two imperfect palindromes were present in each of the promoters (189, 247, 255). For XylR, the UAS is localized between bp 127 and 172 from the Pu transcription start site and between bp 139 and 184 from Ps. The DmpR binding sequences lay between bp 126 and 171 from the Po promoter, whereas those for HbpR are located between bp 180 and 227 on the hbpC promoter and between bp 168 and 225 on the hbpD promoter (96, 255). A second set of HbpR-UAS is present in the intergenic region between hbpR and hbpC (bp 494 to 540), which is improperly positioned to act on the hbpC promoter but which was shown to be important for hbpR autoregulation (96). The two palindromic sequences in the promoter are approximately 16 bp long with a spacing of 29 to 42 bp between the centers of the palindromes.
XylR-
A bound one UAS on the Pu-DNA with higher affinity than it bound the other (189). At that point, the authors suggested that this could mean that two dimers bound the two binding sites independently. However, in the case of HbpR, both palindromic sequences were simultaneously needed for binding, since fragments containing only one were not maintained in a stable protein-DNA complex in gel mobility shift assays (255). Adding 2-hydroxybiphenyl and ATP resulted in a twofold change in binding affinity of HbpR to the promoter DNA (255). DNase I footprints of the Pu UAS fragment with purified XylR-
A and ATP showed an occupation and slightly expanded protected region of the UAS at lower protein concentrations compared to those in the assay without ATP (186). ATP hydrolysis itself is not required for occupation of the UASs by XylR, since the use of ATP
S, which in contrast to ATP, is not hydrolyzable, gave rise to identical footprinting patterns to those for ATP (186). This would be in agreement with the binding of a higher-order oligomeric form. In vivo footprinting of the Pu promoter showed that the presence of the inducer slightly altered the interaction between XylR and the DNA (1). More recently, Valls and de Lorenzo repeated the in vivo footprinting with a single-copy xylR gene and the Pu promoter (258). Their results showed that XylR interacts only very transiently with its binding site, with hardly any protection visible under both uninduced and induced conditions. In fact, the estimated number of XylR hexamers is around 5 to 30 per individual cell under stationary-phase conditions (65). This would equal a concentration of 10 to 50 nM, which is quite low compared to the 400 nM XylR-
A required to protect the DNA in in vitro DNase I footprints. However, it is clear that most static DNA binding studies fully neglect the kinetic aspects of the regulatory cycle in the microbes themselves.

PROSPECTS
As a result of many studies during the past decade, we now have
a much better understanding of the behavior of different regulatory
proteins in the process of mediating transcription. Although
a few pivotal regulatory proteins in classical degradation pathways
for aromatic compounds (i.e., XylS, XylR, and DmpR) have resisted
purification, the solution state could be deduced for several
others, sometimes in the presence of the DNA binding regions.
In some cases it has been possible to deduce the structural
changes induced in the protein or protein-DNA complex by the
chemical effector. In contrast, little is currently known about
the interactions between the regulatory protein and the effector
compounds. The effector binding pockets and effector binding
affinities are not well defined, and it is not clear how effector
binding to the regulatory protein transmits to an "activation"
signal for RNAP.
Although a relatively clear picture has emerged for the different components of the regulatory machineries, their interactions with the operator DNA and with RNA polymerase or with other auxiliary protein factors, and the types of signaling molecules, the picture is mostly static. Most models suggest a regulatory protein which is bound to its DNA binding site and ready to activate transcription (or disappear after derepression). Clear indications for XylR/DmpR-type regulators point at a cyclic model between the inactive regulator state and the active (multimeric) state, but with an equilibrium toward the inactive state and very little site occupancy by XylR. We might thus be very surprised to find our ideas about the activation (or derepression) processes changing when more kinetic or affinity equilibria data become available.
Our current perspective on regulatory systems is most probably somewhat biased by the choice of traditionally studied microorganisms with degradation capacities, such as Pseudomonas, Acinetobacter, Ralstonia, and Burkholderia, typical members of the Gamma- and Betaproteobacteria. It might very well be that new interesting systems are discovered, such as the two FNR-like and one MarR-like regulatory proteins in Rhodopseudomonas which control benzene degradation under anaerobic conditions. Also, regulatory proteins with possible membrane-spanning domains (such as BpdS) or with association with transport and chemotaxis (such as NahY of P. putida) (80) may provide very new insights in how bacteria accomplish recognition and expression regulation of aromatic degradation pathways. In the end and from an environmental perspective, it will again be necessary to refocus on the strategies used by bacteria to recognize and utilize aromatic compounds (or other polluting chemicals) at very low concentration ranges (micromolar or lower). Although in the laboratory we like to feed our pet microorganisms with much higher doses (millimolar), the organisms in their natural environments have to cope with very low carbon compound fluxes or (at best) fluctuating levels. Are regulatory proteins sufficiently sensitive to react and mediate specific catabolic gene expression under these conditions, or are the organisms using alternative strategies to metabolize low carbon fluxes? Gene expression data for the 2,4-dichlorophenoxyacetate degradative pathway in R. eutropha, for example, have suggested that only very slight bursts of transcription activation take place at 10 µM 2,4-dichlorophenoxyacetate (127). Similar experiments with S. paucimobilis have not shown any measurable gene induction of the lin pathway at 3 µM lindane (M. Suar, J. R. van der Meer, K. Lawlor, C. Holliger, and R. Lal, submitted for publication) but, rather, a low constitutive expression. Interestingly, a very clear difference exists between the apparent effector binding affinity of heavy-metal-responsive regulatory proteins (nano- to micromolar range) and those responsive to aromatic compounds (usually micromolar) (95). Obtaining a better view of the differences in the molecular binding affinities of the effector compounds to the regulator and the role of DNA binding in the affinity of effector binding may help to resolve this apparent mystery. This will also be an important challenge for the application of bacterial regulatory systems for the construction of environmental quality sensors, which should have sensitivities below micromolar concentrations.

ACKNOWLEDGMENTS
We thank Victor de Lorenzo for critically reading the manuscript.
We also gratefully acknowledge the many detailed suggestions
by two unknown reviewers, which have helped to improve the manuscript.
Part of this work was financed under the EU 5th Framework Program, BIOCARTE contract QLK3-CT-2002-01923, and by the Swiss Federal Office for Education and Science.

FOOTNOTES
* Corresponding author. Mailing address: Department of Fundamental Microbiology, BÂtiment de Biologie, University of Lausanne, CH 1015 Lausanne, Switzerland. Phone: 41 21 692 5630. Fax: 41 21 692 5605. E-mail:
JanRoelof.VanderMeer{at}imf.unil.ch.


REFERENCES
- 1 Abril, M. A., M. Buck, and J. L. Ramos. 1991. Activation of the Pseudomonas TOL plasmid upper pathway operon. Identification of binding sites for the positive regulator XylR and for integration host factor protein. J. Biol. Chem. 266:15832-15838.[Abstract/Free Full Text]
- 2 Abril, M. A., C. Michan, K. N. Timmis, and J. L. Ramos. 1989. Regulator and enzyme specificities of the TOL plasmid-encoded upper pathway for degradation of aromatic hydrocarbons and expansion of the substrate range of the pathway. J. Bacteriol. 171:6782-6790.[Abstract/Free Full Text]
- 3 Achong, G. R., A. M. Rodriguez, and A. M. Spormann. 2001. Benzylsuccinate synthase of Azoarcus sp. strain T: cloning, sequencing, transcriptional organization, and its role in anaerobic toluene and m-xylene mineralization. J. Bacteriol. 183:6763-6770.[Abstract/Free Full Text]
- 4 Alekshun, M. N., S. B. Levy, T. R. Mealy, B. A. Seaton, and J. F. Head. 2001. The crystal structure of MarR, a regulator of multiple antibiotic resistance, at 2.3 Å resolution. Nat. Struct. Biol. 8:710-714.[CrossRef][Medline]
- 5 Alex, L. A., and M. I. Simon. 1994. Protein histidine kinases and signal transduction in prokaryotes and eukaryotes. Trends Genet. 10:133-138.[CrossRef][Medline]
- 6 Ansari, A. Z., J. E. Bradner, and T. V. O'Halloran. 1995. DNA-bend modulation in a repressor-to-activator switching mechanism. Nature 374:371-375.[Medline]
- 7 Arai, H., S. Akahira, T. Ohishi, and T. Kudo. 1999. Adaptation of Comamonas testosteroni TA441 to utilization of phenol by spontaneous mutation of the gene for a trans-acting factor. Mol. Microbiol. 33:1132-1140.[CrossRef][Medline]
- 8 Arai, H., S. Akahira, T. Ohishi, M. Maeda, and T. Kudo. 1998. Adaptation of Comamonas testosteroni TA441 to utilize phenol: organization and regulation of the genes involved in phenol degradation. Microbiology 144:2895-2903.[Abstract]
- 9 Arenghi, F. L., P. Barbieri, G. Bertoni, and V. de Lorenzo. 2001. New insights into the activation of o-xylene biodegradation in Pseudomonas stutzeri OX1 by pathway substrates. EMBO Rep. 2:409-414.[CrossRef][Medline]
- 10 Arenghi, F. L., D. Berlanda, E. Galli, G. Sello, and P. Barbieri. 2001. Organization and regulation of meta cleavage pathway genes for toluene and o-xylene derivative degradation in Pseudomonas stutzeri OX1. Appl. Environ. Microbiol. 67:3304-3308.[Abstract/Free Full Text]
- 11 Arenghi, F. L., M. Pinti, E. Galli, and P. Barbieri. 1999. Identification of the Pseudomonas stutzeri OX1 toluene-o-xylene monooxygenase regulatory gene (touR) and of its cognate promoter. Appl. Environ. Microbiol. 65:4057-4063.[Abstract/Free Full Text]
- 12 Bates, D. M., C. V. Popescu, N. Khoroshilova, K. Vogt, H. Beinert, E. Munck, and P. J. Kiley. 2000. Substitution of leucine 28 with histidine in the Escherichia coli transcription factor FNR results in increased stability of the [4Fe-4S]2+ cluster to oxygen. J. Biol. Chem. 275:6234-6240.[Abstract/Free Full Text]
- 13 Bertani, I., M. Kojic, and V. Venturi. 2001. Regulation of the p-hydroxybenzoic acid hydroxylase gene (pobA) in plant-growth-promoting Pseudomonas putida WCS358. Microbiology 147:1611-1620.[Abstract/Free Full Text]
- 14 Bertoni, G., S. Marqués, and V. de Lorenzo. 1998. Activation of the toluene-responsive regulator XylR causes a transcriptional switch between
54 and
70 promoters at the divergent Pr/Ps region of the TOL plasmid. Mol. Microbiol. 27:651-659.[CrossRef][Medline]
- 15 Bhende, P. M., and S. M. Egan. 2000. Genetic evidence that transcription activation by RhaS involves specific amino acid contacts with
70. J. Bacteriol. 182:4959-4969.[Abstract/Free Full Text]
- 16 Brzostowicz, P. C., A. B. Reams, T. J. Clark, and E. L. Neidle. 2003. Transcriptional cross-regulation of the catechol and protocatechuate branches of the ß-ketoadipate pathway contributes to carbon source-dependent expression of the Acinetobacter sp. strain ADP1 pobA gene. Appl. Environ. Microbiol. 69:1598-1606.[Abstract/Free Full Text]
- 17 Buck, M., and W. Cannon. 1992. Activator-independent formation of a closed complex between
54-holoenzyme and nifH and nifU promoters of Klebsiella pneumoniae. Mol. Microbiol. 6:1625-1630.[CrossRef][Medline]
- 18 Buck, M., and W. Cannon. 1992. Specific binding of the transcription factor
54 to promoter DNA. Nature 358:422-424.[CrossRef][Medline]
- 19 Buck, M., W. Cannon, and J. Woodcock. 1987. Transcriptional activation of the Klebsiella pneumoniae nitrogenase promoter may involve DNA loop formation. Mol. Microbiol. 1:243-249.[CrossRef][Medline]
- 20 Bundy, B. M., L. S. Collier, T. R. Hoover, and E. L. Neidle. 2002. Synergistic transcriptional activation by one regulatory protein in response to two metabolites. Proc. Natl. Acad. Sci. USA 99:7693-7698.[Abstract/Free Full Text]
- 21 Bustos, S. A., and R. F. Schleif. 1993. Functional domains of the AraC protein. Proc. Natl. Acad. Sci. USA 90:5638-5642.[Abstract/Free Full Text]
- 22 Byrne, A. M., and R. H. Olsen. 1996. Cascade regulation of the toluene-3- monooxygenase operon (tbuA1UBVA2C) of Burkholderia pickettii PKO1: role of the tbuA1 promoter (PtbuA1) in the expression of its cognate activator, TbuT. J. Bacteriol. 178:6327-6337.[Abstract/Free Full Text]
- 23 Cases, I., and V. de Lorenzo. 2001. The black cat/white cat principle of signal integration in bacterial promoters. EMBO J. 20:1-11.[CrossRef][Medline]
- 24 Caswell, R., J. Williams, A. Lyddiatt, and S. Busby. 1992. Overexpression, purification and characterization of the Escherichia coli MelR transcription activator protein. Biochem. J. 287:493-499.[Medline]
- 25 Chaney, M., R. Grande, S. R. Wigneshweraraj, W. Cannon, P. Casaz, M. T. Gallegos, J. Schumacher, S. Jones, S. Elderkin, A. E. Dago, E. Morett, and M. Buck. 2001. Binding of transcriptional activators to
54 in the presence of the transition state analog ADP-aluminum fluoride: insights into activator mechanochemical action. Genes Dev. 15:2282-2294.[Abstract/Free Full Text]
- 26 Choi, E. N., M. C. Cho, Y. Kim, C. K. Kim, and K. Lee. 2003. Expansion of growth substrate range in Pseudomonas putida F1 by mutations in both cymR and todS, which recruit a ring-fission hydrolase CmtE and induce the tod catabolic operon, respectively. Microbiology 149:795-805.[Abstract/Free Full Text]
- 27 Chugani, S. A., M. R. Parsek, and A. M. Chakrabarty. 1998. Transcriptional repression mediated by LysR-type regulator CatR bound at multiple binding sites. J. Bacteriol. 180:2367-2372.[Abstract/Free Full Text]
- 28 Chugani, S. A., M. R. Parsek, C. D. Hershberger, K. Murakami, A. Ishihama, and A. M. Chakrabarty. 1997. Activation of the catBCA promoter: probing the interaction of CatR and RNA polymerase through in vitro transcription. J. Bacteriol. 179:2221-2227.[Abstract/Free Full Text]
- 29 Clark, T. J., S. Haddad, E. L. Neidle, and C. Momany. 2004. Crystallization of the effector-binding domains of BenM and CatM, LysR-type transcriptional regulators from Acinetobacter sp. ADP1. Acta Crystallogr. Ser. D 60:105-108.[CrossRef][Medline]
- 30 Clark, T. J., C. Momany, and E. L. Neidle. 2002. The benPK operon, proposed to play a role in transport, is part of a regulon for benzoate catabolism in Acinetobacter sp. strain ADP1. Microbiology 148:1213-1223.[Abstract/Free Full Text]
- 31 Clark, T. J., R. S. Phillips, B. M. Bundy, C. Momany, and E. L. Neidle. 2004. Benzoate decreases the binding of cis,cis-muconate to the BenM regulator despite the synergistic effect of both compounds on transcriptional activation. J. Bacteriol. 186:1200-1204.[Abstract/Free Full Text]
- 32 Coco, W. M., M. R. Parsek, and A. M. Chakrabarty. 1994. Purification of the LysR family regulator, ClcR, and its interaction with the Pseudomonas putida clcABD chlorocatechol operon promoter. J. Bacteriol. 176:5530-5533.[Abstract/Free Full Text]
- 33 Coco, W. M., R. K. Rothmel, S. Henikoff, and A. M. Chakrabarty. 1993. Nucleotide sequence and initial functional characterization of the clcR gene encoding a LysR family activator of the clcABD chlorocatechol operon in Pseudomonas putida. J. Bacteriol. 175:417-427.[Abstract/Free Full Text]
- 34 Collier, L. S., G. L. Gaines, and E. L. Neidle. 1998. Regulation of benzoate degradation in Acinetobacter sp. strain ADP1 by BenM, a LysR-type transcriptional activator. J. Bacteriol. 180:2493-2501.[Abstract/Free Full Text]
- 35 Coschigano, P. W., and L. Y. Young. 1997. Identification and sequence analysis of two regulatory genes involved in anaerobic toluene metabolism by strain T1. Appl. Environ. Microbiol. 63:652-660.[Abstract]
- 36 Cowles, C. E., N. N. Nichols, and C. S. Harwood. 2000. BenR, a XylS homologue, regulates three different pathways of aromatic acid degradation in Pseudomonas putida. J. Bacteriol. 182:6339-6346.[Abstract/Free Full Text]
- 37 Da Re, S., J. Schumacher, P. Rousseau, J. Fourment, C. Ebel, and D. Kahn. 1999. Phosphorylation-induced dimerization of the FixJ receiver domain. Mol. Microbiol. 34:504-511.[CrossRef][Medline]
- 38 Delgado, A., and J. L. Ramos. 1994. Genetic evidence for activation of the positive transcriptional regulator XylR, a member of the NtrC family of regulators, by effector binding. J. Biol. Chem. 269:8059-8062.[Abstract/Free Full Text]
- 39 de Lorenzo, V., and J. Pérez-Martin. 1996. Regulatory noise in prokaryotic promoters: how bacteria learn to respond to novel environmental signals. Mol. Microbiol. 19:1177-1184.[CrossRef][Medline]
- 40 Deo, P. G., and N. G. Karanth. 1994. Biodegradation of hexachlorocyclohexane isomers in soil and food environment. Crit. Rev. Microbiol. 20:57-78.[Medline]
- 41 Devos, D., J. Garmendia, V. de Lorenzo, and A. Valencia. 2002. Deciphering the action of aromatic effectors on the prokaryotic enhancer-binding protein XylR: a structural model of its N-terminal domain. Environ. Microbiol. 4:29-41.[CrossRef][Medline]
- 42 Diaz, E., A. Ferrández, and J. L. García. 1998. Characterization of the hca cluster encoding the dioxygenolytic pathway for initial catabolism of 3-phenylpropionic acid in Escherichia coli K-12. J. Bacteriol. 180:2915-2923.[Abstract/Free Full Text]
- 43 Díaz, E., A. Ferrández, M. A. Prieto, and J. L. García. 2001. Biodegradation of aromatic compounds by Escherichia coli. Microbiol. Mol. Biol. Rev. 65:523-569.[Abstract/Free Full Text]
- 44 Díaz, E., and M. A. Prieto. 2000. Bacterial promoters triggering biodegradation of aromatic pollutants. Curr. Opin. Biotechnol. 11:467-475.[CrossRef][Medline]
- 45 DiMarco, A. A., B. Averhoff, and L. N. Ornston. 1993. Identification of the transcriptional activator pobR and characterization of its role in the expression of pobA, the structural gene for p-hydroxybenzoate hydroxylase in Acinetobacter calcoaceticus. J. Bacteriol. 175:4499-4506.[Abstract/Free Full Text]
- 46 DiMarco, A. A., and L. N. Ornston. 1994. Regulation of p-hydroxybenzoate hydroxylase synthesis by PobR bound to an operator in Acinetobacter calcoaceticus. J. Bacteriol. 176:4277-4284.[Abstract/Free Full Text]
- 47 Dixon, R. 1986. The xylABC promoter from the Pseudomonas putida TOL plasmid is activated by nitrogen regulatory genes in Escherichia coli. Mol. Gen. Genet. 203:129-136.[CrossRef][Medline]
- 48 Donald, L. J., D. J. Hosfield, S. L. Cuvelier, W. Ens, K. G. Standing, and H. W. Duckworth. 2001. Mass spectrometric study of the Escherichia coli repressor proteins, IclR and GclR, and their complexes with DNA. Protein Sci. 10:1370-1380.[Abstract/Free Full Text]
- 49 Dua, M., A. Singh, N. Sethunathan, and A. K. Johri. 2002. Biotechnology and bioremediation: successes and limitations. Appl. Microbiol. Biotechnol. 59:143-152.[CrossRef][Medline]
- 50 Eaton, R. W. 1997. p-Cymene catabolic pathway in Pseudomonas putida F1: cloning and characterization of DNA encoding conversion of p-cymene to p-cumate. J. Bacteriol. 179:3171-3180.[Abstract/Free Full Text]
- 51 Eaton, R. W., O. V. Selifonova, and R. M. Gedney. 1998. Isopropylbenzene catabolic pathway in Pseudomonas putida RE204: nucleotide sequence analysis of the ipb operon and neighboring DNA from pRE4. Biodegradation 9:119-132.[CrossRef][Medline]
- 52 Egan, S. M. 2002. Growing repertoire of AraC/XylS activators. J. Bacteriol. 184:5529-5532.[Free Full Text]
- 53 Egan, S. M., A. J. Pease, J. Lang, X. Li, V. Rao, W. K. Gillette, R. Ruiz, J. L. Ramos, and R. E. Wolf, Jr. 2000. Transcription activation by a variety of AraC/XylS family activators does not depend on the class II-specific activation determinant in the N-terminal domain of the RNA polymerase alpha subunit. J. Bacteriol. 182:7075-7077.[Abstract/Free Full Text]
- 54 Egger, L. A., H. Park, and M. Inouye. 1997. Signal transduction via the histidyl-aspartyl phosphorelay. Genes Cells 2:167-184.[Abstract]
- 55 Egland, P. G., and C. S. Harwood. 1999. BadR, a new MarR family member, regulates anaerobic benzoate degradation by Rhodopseudomonas palustris in concert with AadR, an FNR family member. J. Bacteriol. 181:2102-2109.[Abstract/Free Full Text]
- 56 Egland, P. G., and C. S. Harwood. 2000. HbaR, a 4-hydroxybenzoate sensor and FNR-CRP superfamily member, regulates anaerobic 4-hydroxybenzoate degradation by Rhodopseudomonas palustris. J. Bacteriol. 182:100-106.[Abstract/Free Full Text]
- 57 Ellis, L. B., B. K. Hou, W. Kang, and L. P. Wackett. 2003. The University of Minnesota Biocatalysis/Biodegradation Database: post-genomic data mining. Nucleic Acids Res. 31:262-265.[Abstract/Free Full Text]
- 58 Eulberg, D., S. Lakner, L. A. Golovleva, and M. Schlömann. 1998. Characterization of a protocatechuate catabolic gene cluster from Rhodococcus opacus 1CP: evidence for a merged enzyme with 4-carboxymuconolactone-decarboxylating and 3-oxoadipate enol-lactone-hydrolyzing activity. J. Bacteriol. 180:1072-1081.[Abstract/Free Full Text]
- 59 Eulberg, D., and M. Schlömann. 1998. The putative regulator of catechol catabolism in Rhodococcus opacus 1CP-an IclR-type, not a LysR-type transcriptional regulator. Antonie Leeuwenhoek 74:71-82.[CrossRef][Medline]
- 60 Evans, P. J., D. T. Mang, K. S. Kim, and L. Y. Young. 1991. Anaerobic degradation of toluene by a denitrifying bacterium. Appl. Environ. Microbiol. 57:1139-1145.[Abstract/Free Full Text]
- 61 Ferrández, A., J. L. Garcia, and E. Díaz. 1997. Genetic characterization and expression in heterologous hosts of the 3-(3-hydroxyphenyl)propionate catabolic pathway of Escherichia coli K-12. J. Bacteriol. 179:2573-2581.[Abstract/Free Full Text]
- 62 Ferrández, A., J. L. Garcia, and E. Díaz. 2000. Transcriptional regulation of the divergent paa catabolic operons for phenylacetic acid degradation in Escherichia coli. J. Biol. Chem. 275:12214-12222.[Abstract/Free Full Text]
- 63 Ferrández, A., B. Miñambres, B. Garcia, E. R. Olivera, J. M. Luengo, J. L. García, and E. Díaz. 1998. Catabolism of phenylacetic acid in Escherichia coli. Characterization of a new aerobic hybrid pathway. J. Biol. Chem. 273:25974-25986.[Abstract/Free Full Text]
- 64 Fiedler, U., and V. Weiss. 1995. A common switch in activation of the response regulators NtrC and PhoB: phosphorylation induces dimerization of the receiver modules. EMBO J. 14:3696-3705.[Medline]
- 65 Fraile, S., F. Roncal, L. A. Fernández, and V. de Lorenzo. 2001. Monitoring intracellular levels of XylR in Pseudomonas putida with a single-chain antibody specific for aromatic-responsive enhancer-binding proteins. J. Bacteriol. 183:5571-5579.[Abstract/Free Full Text]
- 66 Franklin, F. C., P. R. Lehrbach, R. Lurz, B. Rückert, M. Bagdasarian, and K. N. Timmis. 1983. Localization and functional analysis of transposon mutations in regulatory genes of the TOL catabolic pathway. J. Bacteriol. 154:676-685.[Abstract/Free Full Text]
- 67 Fukumori, F., and C. P. Saint. 1997. Nucleotide sequences and regulational analysis of genes involved in conversion of aniline to catechol in Pseudomonas putida UCC22(pTDN1). J. Bacteriol. 179:399-408.[Abstract/Free Full Text]
- 68 Galan, B., A. Kolb, J. M. Sanz, J. L. García, and M. A. Prieto. 2003. Molecular determinants of the hpa regulatory system of Escherichia coli: the HpaR repressor. Nucleic Acids Res. 31:6598-6609.[Abstract/Free Full Text]
- 69 Gallegos, M. T., S. Marqués, and J. L. Ramos. 1996. Expression of the TOL plasmid xylS gene in Pseudomonas putida occurs from a
70-dependent promoter or from
70- and
54-dependent tandem promoters according to the compound used for growth. J. Bacteriol. 178:2356-2361.[Abstract/Free Full Text]
- 70 Gallegos, M. T., S. Marqués, and J. L. Ramos. 1996. The TACAN4TGCA motif upstream from the 35 region in the
70-
s-dependent Pm promoter of the TOL plasmid is the minimum DNA segment required for transcription stimulation by XylS regulators. J. Bacteriol. 178:6427-6434.[Abstract/Free Full Text]
- 71 Gallegos, M. T., R. Schleif, A. Bairoch, K. Hofmann, and J. L. Ramos. 1997. Arac/XylS family of transcriptional regulators. Microbiol. Mol. Biol. Rev. 61:393-410.[Abstract]
- 72 Garmendia, J., and V. de Lorenzo. 2000. The role of the interdomain B linker in the activation of the XylR protein of Pseudomonas putida. Mol. Microbiol. 38:401-410.[CrossRef][Medline]
- 73 Garmendia, J., D. Devos, A. Valencia, and V. de Lorenzo. 2001. A la carte transcriptional regulators: unlocking responses of the prokaryotic enhancer-binding protein XylR to non-natural effectors. Mol. Microbiol. 42:47-59.[CrossRef][Medline]
- 74 Gentz, R., F. J. Rauscher, C. Abate, and T. Curran. 1989. Parallel association of Fos and Jun leucine zippers juxtaposes DNA binding domains. Science 243:1695-1699.[Abstract/Free Full Text]
- 75 Gerischer, U., A. Segura, and L. N. Ornston. 1998. PcaU, a transcriptional activator of genes for protocatechuate utilization in Acinetobacter. J. Bacteriol. 180:1512-1524.[Abstract/Free Full Text]
- 76 Gibson, J., and C. S. Harwood. 2002. Metabolic diversity in aromatic compound utilization by anaerobic microbes. Annu. Rev. Microbiol. 56:345-369.[CrossRef][Medline]
- 77 Gonzalez-Pérez, M. M., S. Marqués, P. Dominguez-Cuevas, and J. L. Ramos. 2002. XylS activator and RNA polymerase binding sites at the Pm promoter overlap. FEBS Lett. 519:117-122.[CrossRef][Medline]
- 78 Gonzalez-Pérez, M. M., J. L. Ramos, M. T. Gallegos, and S. Marqués. 1999. Critical nucleotides in the upstream region of the XylS-dependent TOL meta-cleavage pathway operon promoter as deduced from analysis of mutants. J. Biol. Chem. 274:2286-2290.[Abstract/Free Full Text]
- 79 Gralla, J. D. 1996. Activation and repression of E. coli promoters. Curr. Opin. Genet. Dev. 6:526-530.[CrossRef][Medline]
- 80 Grimm, A. C., and C. S. Harwood. 1999. NahY, a catabolic plasmid-encoded receptor required for chemotaxis of Pseudomonas putida to the aromatic hydrocarbon naphthalene. J. Bacteriol. 181:3310-3316.[Abstract/Free Full Text]
- 81 Guo, Z., and J. E. Houghton. 1999. PcaR-mediated activation and repression of pca genes from Pseudomonas putida are propagated by its binding to both the 35 and the 10 promoter elements. Mol. Microbiol. 32:253-263.[CrossRef][Medline]
- 82 Harwood, C. S., and R. E. Parales. 1996. The ß-ketoadipate pathway and the biology of self-identity. Annu. Rev. Microbiol. 50:553-590.[CrossRef][Medline]
- 83 Haydon, D. J., and J. R. Guest. 1991. A new family of bacterial regulatory proteins. FEMS Microbiol. Lett. 63:291-295.[Medline]
- 84 Henikoff, S., G. W. Haughn, J. M. Calvo, and J. C. Wallace. 1988. A large family of bacterial activator proteins. Proc. Natl. Acad. Sci. USA 85:6602-6606.[Abstract/Free Full Text]
- 85 Hidalgo, E., and B. Demple. 1997. Spacing of promoter elements regulates the basal expression of the soxS gene and converts SoxR from a transcriptional activator into a repressor. EMBO J. 16:1056-1065.[CrossRef][Medline]
- 86 Hindle, Z., and C. P. Smith. 1994. Substrate induction and catabolite repression of the Streptomyces coelicolor glycerol operon are mediated through the GylR protein. Mol. Microbiol. 12:737-745.[CrossRef][Medline]
- 87 Hohnstock, A. M., K. G. Stuart-Keil, E. E. Kull, and E. L. Madsen. 2000. Naphthalene and donor cell density influence field conjugation of naphthalene catabolism plasmids. Appl. Environ. Microbiol. 66:3088-3092.[Abstract/Free Full Text]
- 88 Hryniewicz, M. M., and N. M. Kredich. 1994. Stoichiometry of binding of CysB to the cysJIH, cysK, and cysP promoter regions of Salmonella typhimurium. J. Bacteriol. 176:3673-3682.[Abstract/Free Full Text]
- 89 Huang, K. J., C. Y. Lan, and M. M. Igo. 1997. Phosphorylation stimulates the cooperative DNA-binding properties of the transcription factor OmpR. Proc. Natl. Acad. Sci. USA 94:2828-2832.[Abstract/Free Full Text]
- 90 Hughes, E. J., M. K. Shapiro, J. E. Houghton, and L. N. Ornston. 1988. Cloning and expression of pca genes from Pseudomonas putida in Escherichia coli. J. Gen. Microbiol. 134:2877-2887.[Medline]
- 91 Inouye, S., A. Nakazawa, and T. Nakazawa. 1987. Expression of the regulatory gene xylS on the TOL plasmid is positively controlled by the xylR gene product. Proc. Natl. Acad. Sci. USA 84:5182-5186.[Abstract/Free Full Text]
- 92 Inouye, S., A. Nakazawa, and T. Nakazawa. 1981. Molecular cloning of gene xylS of the TOL plasmid: evidence for positive regulation of the xylDEGF operon by xylS. J. Bacteriol. 148:413-418.[Abstract/Free Full Text]
- 93 Inouye, S., A. Nakazawa, and T. Nakazawa. 1986. Nucleotide sequence of the regulatory gene xylS on the Pseudomonas putida TOL plasmid and identification of the protein product. Gene 44:235-242.[CrossRef][Medline]
- 94 Inouye, S., A. Nakazawa, and T. Nakazawa. 1987. Overproduction of the xylS gene product and activation of the xylDLEGF operon on the TOL plasmid. J. Bacteriol. 169:3587-3592.[Abstract/Free Full Text]
- 95 Jaspers, M. C. M. 2002. Using reporter bacteria to study the bioavailability of pollutants in aqueous environments. Ph.D. thesis. Swiss Federal Institute of Technology, Zürich, Switzerland.
- 96 Jaspers, M. C. M., C. Meier, A. J. B. Zehnder, H. Harms, and J. R. van der Meer. 2001. Measuring mass transfer processes of octane with the help of an alkSalkB::gfp-tagged Escherichia coli. Environ. Microbiol. 3:512-524.[CrossRef][Medline]
- 97 Jaspers, M. C. M., W. A. Suske, A. Schmid, D. A. Goslings, H.-P. E. Kohler, and J. R. van der Meer. 2000. HbpR, a new member of the XylR/DmpR subclass within the NtrC family of bacterial transcriptional activators, regulates expression of 2-hydroxybiphenyl metabolism in Pseudomonas azelaica HBP1. J. Bacteriol. 182:405-417.[Abstract/Free Full Text]
- 98 Johnson, G. R., and R. H. Olsen. 1997. Multiple pathways for toluene degradation in Burkholderia sp. strain JS150. Appl. Environ. Microbiol. 63:4047-4052.[Abstract]
- 99 Johnson, G. R., and J. C. Spain. 2003. Evolution of catabolic pathways for synthetic compounds: bacterial pathways for degradation of 2,4-dinitrotoluene and nitrobenzene. Appl. Microbiol. Biotechnol. 62:110-123.[CrossRef][Medline]
- 100 Jones, R. M., L. S. Collier, E. L. Neidle, and P. A. Williams. 1999. areABC genes determine the catabolism of aryl esters in Acinetobacter sp. strain ADP1. J. Bacteriol. 181:4568-4575.[Abstract/Free Full Text]
- 101 Jones, R. M., V. Pagmantidis, and P. A. Williams. 2000. sal genes determining the catabolism of salicylate esters are part of a supraoperonic cluster of catabolic genes in Acinetobacter sp. strain ADP1. J. Bacteriol. 182:2018-2025.[Abstract/Free Full Text]
- 102 Kaldalu, N., T. Mandel, and M. Ustav. 1996. TOL plasmid transcription factor XylS binds specifically to the Pm operator sequence. Mol. Microbiol. 20:569-579.[CrossRef][Medline]
- 103 Kaldalu, N., U. Toots, V. de Lorenzo, and M. Ustav. 2000. Functional domains of the TOL plasmid transcription factor XylS. J. Bacteriol. 182:1118-1126.[Abstract/Free Full Text]
- 104 Kasak, L., R. Horak, A. Nurk, K. Talvik, and M. Kivisaar. 1993. Regulation of the catechol 1,2-dioxygenase- and phenol monooxygenase-encoding pheBA operon in Pseudomonas putida PaW85. J. Bacteriol. 175:8038-8042.[Abstract/Free Full Text]
- 105 Keasling, J. D. 1999. Gene-expression tools for the metabolic engineering of bacteria. Trends Biotechnol. 17:452-460.[CrossRef][Medline]
- 106 Kelly, M. T., and T. R. Hoover. 1999. Mutant forms of Salmonella typhimurium
54 defective in transcription initiation but not promoter binding activity. J. Bacteriol. 181:3351-3357.[Abstract/Free Full Text]
- 107 Kessler, B., V. de Lorenzo, and K. N. Timmis. 1993. Identification of a cis-acting sequence within the Pm promoter of the TOL plasmid which confers XylS-mediated responsiveness to substituted benzoates. J. Mol. Biol. 230:699-703.[CrossRef][Medline]
- 108 Kiley, P. J., and H. Beinert. 2003. The role of Fe-S proteins in sensing and regulation in bacteria. Curr. Opin. Microbiol. 6:181-185.[CrossRef][Medline]
- 109 Kitagawa, W., S. Takami, K. Miyauchi, E. Masai, Y. Kamagata, J. M. Tiedje, and M. Fukuda. 2002. Novel 2,4-dichlorophenoxyacetic acid degradation genes from oligotrophic Bradyrhizobium sp. strain HW13 isolated from a pristine environment. J. Bacteriol. 184:509-518.[Abstract/Free Full Text]
- 110 Klose, K. E., A. K. North, K. M. Stedman, and S. Kustu. 1994. The major dimerization determinants of the nitrogen regulatory protein NtrC from enteric bacteria lie in its carboxy-terminal domain. J. Mol. Biol. 241:233-245.[CrossRef][Medline]
- 111 Kohler, T., S. Harayama, J. L. Ramos, and K. N. Timmis. 1989. Involvement of Pseudomonas putida RpoN sigma factor in regulation of various metabolic functions. J. Bacteriol. 171:4326-4333.[Abstract/Free Full Text]
- 112 Kok, R. G., D. A. D'Argenio, and L. N. Ornston. 1998. Mutation analysis of PobR and PcaU, closely related transcriptional activators in Acinetobacter. J. Bacteriol. 180:5058-5069.[Abstract/Free Full Text]
- 113 Komeda, H., M. Kobayashi, and S. Shimizu. 1996. Characterization of the gene cluster of high-molecular-mass nitrile hydratase (H-NHase) induced by its reaction product in Rhodococcus rhodochrous J1. Proc. Natl. Acad. Sci. USA 93:4267-4272.[Abstract/Free Full Text]
- 114 Kwon, H. J., M. H. Bennik, B. Demple, and T. Ellenberger. 2000. Crystal structure of the Escherichia coli Rob transcription factor in complex with DNA. Nat. Struct. Biol. 7:424-430.[CrossRef][Medline]
- 115 Labbe, D., J. Garnon, and P. C. Lau. 1997. Characterization of the genes encoding a receptor-like histidine kinase and a cognate response regulator from a biphenyl/polychlorobiphenyl-degrading bacterium, Rhodococcus sp. strain M5. J. Bacteriol. 179:2772-2776.[Abstract/Free Full Text]
- 116 Landini, P., J. A. Bown, M. R. Volkert, and S. J. Busby. 1998. Ada protein-RNA polymerase sigma subunit interaction and alpha subunit-promoter DNA interaction are necessary at different steps in transcription initiation at the Escherichia coli Ada and aidB promoters. J. Biol. Chem. 273:13307-13312.[Abstract/Free Full Text]
- 117 Landini, P., and S. J. Busby. 1999. The Escherichia coli Ada protein can interact with two distinct determinants in the
70 subunit of RNA polymerase according to promoter architecture: identification of the target of Ada activation at the alkA promoter. J. Bacteriol. 181:1524-1529.[Abstract/Free Full Text]
- 118 Lau, P. C., Y. Wang, A. Patel, D. Labbe, H. Bergeron, R. Brousseau, Y. Konishi, and M. Rawlings. 1997. A bacterial basic region leucine zipper histidine kinase regulating toluene degradation. Proc. Natl. Acad. Sci. USA 94:1453-1458.[Abstract/Free Full Text]
- 119 Laurie, A. D., and G. Lloyd-Jones. 1999. The phn genes of Burkholderia sp. strain RP007 constitute a divergent gene cluster for polycyclic aromatic hydrocarbon catabolism. J. Bacteriol. 181:531-540.[Abstract/Free Full Text]
- 120 Leahy, J. G., G. R. Johnson, and R. H. Olsen. 1997. Cross-regulation of toluene monooxygenases by the transcriptional activators TbmR and TbuT. Appl. Environ. Microbiol. 63:3736-3739.[Abstract]
- 121 Lee, D. J., H. J. Wing, N. J. Savery, and S. J. Busby. 2000. Analysis of interactions between Activating Region 1 of Escherichia coli FNR protein and the C-terminal domain of the RNA polymerase alpha subunit: use of alanine scanning and suppression genetics. Mol. Microbiol. 37:1032-1040.[CrossRef][Medline]
- 122 Lee, J. H., and T. R. Hoover. 1995. Protein crosslinking studies suggest that Rhizobium meliloti C4-dicarboxylic acid transport protein D, a
45-dependent transcriptional activator, interacts with
45 and the beta subunit of RNA polymerase. Proc. Natl. Acad. Sci. USA 92:9702-9706.[Abstract/Free Full Text]
- 123 Lee, S. Y., A. de La Torre, D. Yan, S. Kustu, B. T. Nixon, and D. E. Wemmer. 2003. Regulation of the transcriptional activator NtrC1: structural studies of the regulatory and AAA+ ATPase domains. Genes Dev. 17:2552-2563.[Abstract/Free Full Text]
- 124 Leoni, L., P. Ascenzi, A. Bocedi, G. Rampioni, L. Castellini, and E. Zennaro. 2003. Styrene-catabolism regulation in Pseudomonas fluorescens ST: phosphorylation of StyR induces dimerization and cooperative DNA-binding. Biochem. Biophys. Res. Commun. 303:926-931.[CrossRef][Medline]
- 125 Lessner, D. J., R. E. Parales, S. Narayan, and D. T. Gibson. 2003. Expression of the nitroarene dioxygenase genes in Comamonas sp. strain JS765 and Acidovorax sp. strain JS42 is induced by multiple aromatic compounds. J. Bacteriol. 185:3895-3904.[Abstract/Free Full Text]
- 126 Leuthner, B., and J. Heider. 1998. A two-component system involved in regulation of anaerobic toluene metabolism in Thauera aromatica. FEMS Microbiol. Lett. 166:35-41.[CrossRef][Medline]
- 127 Leveau, J. H. J., F. König, H.-P. Füchslin, C. Werlen, and J. R. van der Meer. 1999. Dynamics of multigene expression during catabolic adaptation of Ralstonia eutropha JMP134(pJP4) to the herbicide 2,4-dichlorophenoxyacetate. Mol. Microbiol. 33:396-406.[CrossRef][Medline]
- 128 Leveau, J. H. J., and J. R. van der Meer. 1996. The tfdR gene product can successfully take over the role of the insertion element-inactivated TfdT protein as a transcriptional activator of the tfdCDEF gene cluster, which encodes chlorocatechol degradation in Ralstonia eutropha JMP134(pJP4). J. Bacteriol. 178:6824-6832.[Abstract/Free Full Text]
- 129 Lewis, R. J., D. J. Scott, J. A. Brannigan, J. C. Ladds, M. A. Cervin, G. B. Spiegelman, J. G. Hoggett, I. Barak, and A. J. Wilkinson. 2002. Dimer formation and transcription activation in the sporulation response regulator Spo0A. J. Mol. Biol. 316:235-245.[CrossRef][Medline]
- 130 Lim, D., K. Poole, and N. C. Strynadka. 2002. Crystal structure of the MexR repressor of the mexRAB-oprM multidrug efflux operon of Pseudomonas aeruginosa. J. Biol. Chem. 277:29253-29259.[Abstract/Free Full Text]
- 131 Lonetto, M. A., V. Rhodius, K. Lamberg, P. Kiley, S. Busby, and C. Gross. 1998. Identification of a contact site for different transcription activators in region 4 of the Escherichia coli RNA polymerase
70 subunit. J. Mol. Biol. 284:1353-1365.[CrossRef][Medline]
- 132 Maloy, S. R., and W. D. Nunn. 1982. Genetic regulation of the glyoxylate shunt in Escherichia coli K-12. J. Bacteriol. 149:173-180.[Abstract/Free Full Text]
- 133 Manzanera, M., S. Marqués, and J. L. Ramos. 2000. Mutational analysis of the highly conserved C-terminal residues of the XylS protein, a member of the AraC family of transcriptional regulators. FEBS Lett. 476:312-317.[CrossRef][Medline]
- 134 Marqués, S., M. T. Gallégos, M. Manzanera, A. Holtel, K. N. Timmis, and J. L. Ramos. 1998. Activation and repression of transcription at the double tandem divergent promoters for the xylR and xylS genes of the TOL plasmid of Pseudomonas putida. J. Bacteriol. 180:2889-2894.[Abstract/Free Full Text]
- 135 Marqués, S., M. T. Gallégos, and J. L. Ramos. 1995. Role of
s in transcription from the positively controlled Pm promoter of the TOL plasmid of Pseudomonas putida. Mol. Microbiol. 18:851-857.[CrossRef][Medline]
- 136 Marqués, S., M. Manzanera, M. M. Gonzalez-Pérez, M. T. Gallégos, and J. L. Ramos. 1999. The XylS-dependent Pm promoter is transcribed in vivo by RNA polymerase with
32 or
38 depending on the growth phase. Mol. Microbiol. 31:1105-1113.[CrossRef][Medline]
- 137 Martin, R. G., and J. L. Rosner. 2001. The AraC transcriptional activators. Curr. Opin. Microbiol. 4:132-137.[CrossRef][Medline]
- 138 McFall, S. M., B. Abraham, C. G. Narsolis, and A. M. Chakrabarty. 1997. A tricarboxylic acid cycle intermediate regulating transcription of a chloroaromatic biodegradative pathway: fumarate-mediated repression of the clcABD operon. J. Bacteriol. 179:6729-6735.[Abstract/Free Full Text]
- 139 McFall, S. M., S. A. Chugani, and A. M. Chakrabarty. 1998. Transcriptional activation of the catechol and chlorocatechol operons: variations on a theme. Gene 223:257-267.[CrossRef][Medline]
- 140 McFall, S. M., T. J. Klem, N. Fujita, A. Ishihama, and A. M. Chakrabarty. 1997. DNase I footprinting, DNA bending and in vitro transcription analyses of ClcR and CatR interactions with the clcABD promoter: evidence of a conserved transcriptional activation mechanism. Mol. Microbiol. 24:965-976.[CrossRef][Medline]
- 141 McFall, S. M., M. R. Parsek, and A. M. Chakrabarty. 1997. 2-Chloromuconate and ClcR-mediated activation of the clcABD operon: in vitro transcriptional and DNase I footprint analyses. J. Bacteriol. 179:3655-3663.[Abstract/Free Full Text]
- 142 Mermod, N., J. L. Ramos, A. Bairoch, and K. N. Timmis. 1987. The xylS gene positive regulator of TOL plasmid pWWO: identification, sequence analysis and overproduction leading to constitutive expression of meta cleavage operon. Mol. Gen. Genet. 207:349-354.[CrossRef][Medline]
- 143 Michán, C., B. Kessler, V. de Lorenzo, K. N. Timmis, and J. L. Ramos. 1992. XylS domain interactions can be deduced from intraallelic dominance in double mutants of Pseudomonas putida. Mol. Gen. Genet. 235:406-412.[CrossRef][Medline]
- 144 Michán, C., L. Zhou, M. T. Gallégos, K. N. Timmis, and J. L. Ramos. 1992. Identification of critical amino-terminal regions of XylS. The positive regulator encoded by the TOL plasmid. J. Biol. Chem. 267:22897-22901.[Abstract/Free Full Text]
- 145 Miller, B. E., and N. M. Kredich. 1987. Purification of the cysB protein from Salmonella typhimurium. J. Biol. Chem. 262:6006-6009.[Abstract/Free Full Text]
- 146 Mishra, V., R. Lal, and Srinivasan. 2001. Enzymes and operons mediating xenobiotic degradation in bacteria. Crit. Rev. Microbiol. 27:133-166.[CrossRef][Medline]
- 147 Miura, K., S. Inouye, and A. Nakazawa. 1998. Protein binding in vivo to OP2 promoter of the Pseudomonas putida TOL plasmid. Biochem. Mol. Biol. Int. 46:933-941.[Medline]
- 148 Miyauchi, K., H. S. Lee, M. Fukuda, M. Takagi, and Y. Nagata. 2002. Cloning and characterization of linR, involved in regulation of the downstream pathway for
-hexachlorocyclohexane degradation in Sphingomonas paucimobilis UT26. Appl. Environ. Microbiol. 68:1803-1807.[Abstract/Free Full Text]
- 149 Morawski, B., A. Segura, and L. N. Ornston. 2000. Repression of Acinetobacter vanillate demethylase synthesis by VanR, a member of the GntR family of transcriptional regulators. FEMS Microbiol. Lett. 187:65-68.[CrossRef][Medline]
- 150 Morett, E., and L. Segovia. 1993. The
54 bacterial enhancer-binding protein family: mechanism of action and phylogenetic relationship of their functional domains. J. Bacteriol. 175:6067-6074.[Free Full Text]
- 151 Mosquéda, G., M. I. Ramos-Gonzalez, and J. L. Ramos. 1999. Toluene metabolism by the solvent-tolerant Pseudomonas putida DOT-T1 strain, and its role in solvent impermeabilization. Gene 232:69-76.[CrossRef][Medline]
- 152 Mouz, S., C. Merlin, D. Springael, and A. Toussaint. 1999. A GntR-like negative regulator of the biphenyl degradation genes of the transposon Tn4371. Mol. Gen. Genet. 262:790-799.[CrossRef][Medline]
- 153 Müller, C., L. Petruschka, H. Cuypers, G. Burchhardt, and H. Herrmann. 1996. Carbon catabolite repression of phenol degradation in Pseudomonas putida is mediated by the inhibition of the activator protein PhlR. J. Bacteriol. 178:2030-2036.[Abstract/Free Full Text]
- 154 Müller, T. A., C. Werlen, J. Spain, and J. R. van der Meer. 2003. Evolution of a chlorobenzene degradative pathway among bacteria in a contaminated groundwater mediated by a genomic island in Ralstonia. Environ. Microbiol. 5:163-173.[CrossRef][Medline]
- 155 Muraoka, S., R. Okumura, N. Ogawa, T. Nonaka, K. Miyashita, and T. Senda. 2003. Crystal structure of a full-length LysR-type transcriptional regulator, CbnR: unusual combination of two subunit forms and molecular bases for causing and changing DNA bend. J. Mol. Biol. 328:555-566.[CrossRef][Medline]
- 156 Nasser, W., S. Reverchon, and J. Robert-Baudouy. 1992. Purification and functional characterization of the KdgR protein, a major repressor of pectinolysis genes of Erwinia chrysanthemi. Mol. Microbiol. 6:257-265.[CrossRef][Medline]
- 157 Neuwald, A. F., L. Aravind, J. L. Spouge, and E. V. Koonin. 1999. AAA+: a class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes. Genome Res. 9:27-43.[Abstract/Free Full Text]
- 158 Ng, L. C., C. L. Poh, and V. Shingler. 1995. Aromatic effector activation of the NtrC-like transcriptional regulator PhhR limits the catabolic potential of the (methyl)phenol degradative pathway it controls. J. Bacteriol. 177:1485-1490.[Abstract/Free Full Text]
- 159 Nichols, N. N., and C. S. Harwood. 1997. PcaK, a high-affinity permease for the aromatic compounds 4-hydroxybenzoate and protocatechuate from Pseudomonas putida. J. Bacteriol. 179:5056-5061.[Abstract/Free Full Text]
- 160 Nichols, N. N., and C. S. Harwood. 1995. Repression of 4-hydroxybenzoate transport and degradation by benzoate: a new layer of regulatory control in the Pseudomonas putida ß-ketoadipate pathway. J. Bacteriol. 177:7033-7040.[Abstract/Free Full Text]
- 161 Nishino, S. F., J. C. Spain, L. A. Belcher, and C. D. Litchfield. 1992. Chlorobenzene degradation by bacteria isolated from contaminated groundwater. Appl. Environ. Microbiol. 58:1719-1726.[Abstract/Free Full Text]
- 162 North, A. K., K. E. Klose, K. M. Stedman, and S. Kustu. 1993. Prokaryotic enhancer-binding proteins reflect eukaryote-like modularity: the puzzle of nitrogen regulatory protein C. J. Bacteriol. 175:4267-4273.[Free Full Text]
- 163 Ogawa, N., S. M. McFall, T. J. Klem, K. Miyashita, and A. M. Chakrabarty. 1999. Transcriptional activation of the chlorocatechol degradative genes of Ralstonia eutropha NH9. J. Bacteriol. 181:6697-6705.[Abstract/Free Full Text]
- 164 Ohta, Y., M. Maeda, and T. Kudo. 2001. Pseudomonas putida CE2010 can degrade biphenyl by a mosaic pathway encoded by the tod operon and cmtE, which are identical to those of P. putida F1 except for a single base difference in the operator-promoter region of the cmt operon. Microbiology 147:31-41.[Abstract/Free Full Text]
- 165 Ohtsubo, Y., M. Delawary, K. Kimbara, M. Takagi, A. Ohta, and Y. Nagata. 2001. BphS, a key transcriptional regulator of bph genes involved in polychlorinated biphenyl/biphenyl degradation in Pseudomonas sp. KKS102. J. Biol. Chem. 276:36146-36154.[Abstract/Free Full Text]
- 166 O'Leary, N. D., W. A. Duetz, A. D. Dobson, and K. E. O'Connor. 2002. Induction and repression of the sty operon in Pseudomonas putida CA-3 during growth on phenylacetic acid under organic and inorganic nutrient-limiting continuous culture conditions. FEMS Microbiol. Lett. 208:263-268.[CrossRef][Medline]
- 167 O'Neill, E., L. C. Ng, C. C. Sze, and V. Shingler. 1998. Aromatic ligand binding and intramolecular signalling of the phenol-responsive
54-dependent regulator DmpR. Mol. Microbiol. 28:131-141.[CrossRef][Medline]
- 168 O'Neill, E., C. C. Sze, and V. Shingler. 1999. Novel effector control through modulation of a preexisting binding site of the aromatic-responsive
54-dependent regulator DmpR. J. Biol. Chem. 274:32425-32432.[Abstract/Free Full Text]
- 169 O'Neill, E., P. Wikström, and V. Shingler. 2001. An active role for a structured B-linker in effector control of the
54-dependent regulator DmpR. EMBO J. 20:819-827.[CrossRef][Medline]
- 170 Orth, P., D. Schnappinger, W. Hillen, W. Saenger, and W. Hinrichs. 2000. Structural basis of gene regulation by the tetracycline inducible Tet repressor-operator system. Nat. Struct. Biol. 7:215-219.[CrossRef][Medline]
- 171 Oscarsson, J., Y. Mizunoe, B. E. Uhlin, and D. J. Haydon. 1996. Induction of haemolytic activity in Escherichia coli by the slyA gene product. Mol. Microbiol. 20:191-199.[CrossRef][Medline]
- 172 Osuna, J., X. Soberon, and E. Morett. 1997. A proposed architecture for the central domain of the bacterial enhancer-binding proteins based on secondary structure prediction and fold recognition. Protein Sci. 6:543-555.[Abstract]
- 173 Overhage, J., A. U. Kresse, H. Priefert, H. Sommer, G. Krammer, J. Rabenhorst, and A. Steinbüchel. 1999. Molecular characterization of the genes pcaG and pcaH, encoding protocatechuate 3,4-dioxygenase, which are essential for vanillin catabolism in Pseudomonas sp. strain HR199. Appl. Environ. Microbiol. 65:951-960.[Abstract/Free Full Text]
- 174 Panke, S., B. Witholt, A. Schmid, and M. G. Wubbolts. 1998. Towards a biocatalyst for (S)-styrene oxide production: characterization of the styrene degradation pathway of Pseudomonas sp. strain VLB120. Appl. Environ. Microbiol. 64:2032-2043.[Abstract/Free Full Text]
- 175 Pao, G. M., and M. H. Saier, Jr. 1995. Response regulators of bacterial signal transduction systems: selective domain shuffling during evolution. J. Mol. Evol. 40:136-154.[CrossRef][Medline]
- 176 Park, H. S., and H. S. Kim. 2001. Genetic and structural organization of the aminophenol catabolic operon and its implication for evolutionary process. J. Bacteriol. 183:5074-5081.[Abstract/Free Full Text]
- 177 Park, S. M., H. H. Park, W. K. Lim, and H. J. Shin. 2003. A new variant activator involved in the degradation of phenolic compounds from a strain of Pseudomonas putida. J. Biotechnol. 103:227-236.[CrossRef][Medline]
- 178 Park, W., C. O. Jeon, and E. L. Madsen. 2002. Interaction of NahR, a LysR-type transcriptional regulator, with the
subunit of RNA polymerase in the naphthalene degrading bacterium, Pseudomonas putida NCIB 9816-4. FEMS Microbiol. Lett. 213:159-165.[CrossRef][Medline]
- 179 Parke, D. 1996. Characterization of PcaQ, a LysR-type transcriptional activator required for catabolism of phenolic compounds, from Agrobacterium tumefaciens. J. Bacteriol. 178:266-272.[Abstract/Free Full Text]
- 180 Parke, D., and L. N. Ornston. 2003. Hydroxycinnamate (hca) catabolic genes from Acinetobacter sp. strain ADP1 are repressed by HcaR and are induced by hydroxycinnamoyl-coenzyme A thioesters. Appl. Environ. Microbiol. 69:5398-5409.[Abstract/Free Full Text]
- 181 Parsek, M. R., D. L. Shinabarger, R. K. Rothmel, and A. M. Chakrabarty. 1992. Roles of CatR and cis,cis-muconate in activation of the catBC operon, which is involved in benzoate degradation in Pseudomonas putida. J. Bacteriol. 174:7798-7806.[Abstract/Free Full Text]
- 182 Parsek, M. R., R. W. Ye, P. Pun, and A. M. Chakrabarty. 1994. Critical nucleotides in the interaction of a LysR-type regulator with its target promoter region. catBC promoter activation by CatR. J. Biol. Chem. 269:11279-11284.[Abstract/Free Full Text]
- 183 Pavel, H., M. Forsman, and V. Shingler. 1994. An aromatic effector specificity mutant of the transcriptional regulator DmpR overcomes the growth constraints of Pseudomonas sp. strain CF600 on para-substituted methylphenols. J. Bacteriol. 176:7550-7557.[Abstract/Free Full Text]
- 184 Pelton, J. G., S. Kustu, and D. E. Wemmer. 1999. Solution structure of the DNA-binding domain of NtrC with three alanine substitutions. J. Mol. Biol. 292:1095-1110.[CrossRef][Medline]
- 185 Pérez-Martín, J., and V. de Lorenzo. 1995. The amino-terminal domain of the prokaryotic enhancer-binding protein XylR is a specific intramolecular repressor. Proc. Natl. Acad. Sci. USA 92:9392-9396.[Abstract/Free Full Text]
- 186 Pérez-Martín, J., and V. de Lorenzo. 1996. ATP binding to the
54-dependent activator XylR triggers a protein multimerization cycle catalyzed by UAS DNA. Cell 86:331-339.[CrossRef][Medline]
- 187 Pérez-Martín, J., and V. de Lorenzo. 1996. Identification of the repressor subdomain within the signal reception module of the prokaryotic enhancer-binding protein XylR of Pseudomonas putida. J. Biol. Chem. 271:7899-7902.[Abstract/Free Full Text]
- 188 Pérez-Martín, J., and V. de Lorenzo. 1996. In vitro activities of an N-terminal truncated form of XylR, a
54-dependent transcriptional activator of Pseudomonas putida. J. Mol. Biol. 258:575-587.[CrossRef][Medline]
- 189 Pérez-Martín, J., and V. de Lorenzo. 1996. Physical and functional analysis of the prokaryotic enhancer of the
54-promoters of the TOL plasmid of Pseudomonas putida. J. Mol. Biol. 258:562-574.[CrossRef][Medline]
- 190 Pérez-Martín, J., K. N. Timmis, and V. de Lorenzo. 1994. Co-regulation by bent DNA. Functional substitutions of the integration host factor site at
54-dependent promoter Pu of the upper-TOL operon by intrinsically curved sequences. J. Biol. Chem. 269:22657-22662.[Abstract/Free Full Text]
- 191 Pieper, D. H., and W. Reineke. 2001. Engineering bacteria for bioremediation. Curr. Opin. Biotechnol. 11:262-270.[CrossRef]
- 192 Popham, D. L., D. Szeto, J. Keener, and S. Kustu. 1989. Function of a bacterial activator protein that binds to transcriptional enhancers. Science 243:629-635.[Abstract/Free Full Text]
- 193 Popp, R., T. Kohl, P. Patz, G. Trautwein, and U. Gerischer. 2002. Differential DNA binding of transcriptional regulator PcaU from Acinetobacter sp. strain ADP1. J. Bacteriol. 184:1988-1997.[Abstract/Free Full Text]
- 194 Prieto, M. A., E. Díaz, and J. L. García. 1996. Molecular characterization of the 4-hydroxyphenylacetate catabolic pathway of Escherichia coli W: engineering a mobile aromatic degradative cluster. J. Bacteriol. 178:111-120.[Abstract/Free Full Text]
- 195 Prieto, M. A., and J. L. García. 1997. Identification of a novel positive regulator of the 4-hydroxyphenylacetate catabolic pathway of Escherichia coli. Biochem. Biophys. Res. Commun. 232:759-765.[CrossRef][Medline]
- 196 Prieto, M. A., and J. L. García. 1994. Molecular characterization of 4-hydroxyphenylacetate 3-hydroxylase of Escherichia coli. A two-protein component enzyme. J. Biol. Chem. 269:22823-22829.[Abstract/Free Full Text]
- 197 Providenti, M. A., and R. C. Wyndham. 2001. Identification and functional characterization of CbaR, a MarR-like modulator of the cbaABC-encoded chlorobenzoate catabolism pathway. Appl. Environ. Microbiol. 67:3530-3541.[Abstract/Free Full Text]
- 198 Quinn, J. A., D. B. McKay, and B. Entsch. 2001. Analysis of the pobA and pobR genes controlling expression of p-hydroxybenzoate hydroxylase in Azotobacter chroococcum. Gene 264:77-85.[CrossRef][Medline]
- 199 Raman, N., P. N. Black, and C. C. DiRusso. 1997. Characterization of the fatty acid- responsive transcriptional factor FadR. Biochemical and genetic analyses of the native conformation and functional domains. J. Biol. Chem. 272:30645-30650.[Abstract/Free Full Text]
- 200 Raman, N., and C. C. DiRusso. 1995. Analysis of acyl coenzyme A binding to the transcription factor FadR and identification of amino acid residues in the carboxyl terminus required for ligand binding. J. Biol. Chem. 270:1092-1097.[Abstract/Free Full Text]
- 201 Ramos, J. L., S. Marqués, and K. N. Timmis. 1997. Transcriptional control of the Pseudomonas TOL plasmid catabolic operons is achieved through an interplay of host factors and plasmid-encoded regulators. Annu. Rev. Microbiol. 51:341-373.[CrossRef][Medline]
- 202 Ramos, J. L., N. Mermod, and K. N. Timmis. 1987. Regulatory circuits controlling transcription of TOL plasmid operon encoding meta-cleavage pathway for degradation of alkylbenzoates by Pseudomonas. Mol. Microbiol. 1:293-300.[CrossRef][Medline]
- 203 Ramos, J. L., C. Michán, F. Rojo, D. Dwyer, and K. Timmis. 1990. Signal- regulator interactions. Genetic analysis of the effector binding site of xylS, the benzoate-activated positive regulator of Pseudomonas TOL plasmid meta-cleavage pathway operon. J. Mol. Biol. 211:373-382.[CrossRef][Medline]
- 204 Ramos, J. L., A. Stolz, W. Reineke, and K. N. Timmis. 1986. Altered effector specificities in regulators of gene expression: TOL plasmid xylS mutants and their use to engineer expansion of the range of aromatics degraded by bacteria. Proc. Natl. Acad. Sci. USA 83:8467-8471.[Abstract/Free Full Text]
- 205 Ramos-González, M. I., M. Olson, A. A. Gatenby, G. Mosquéda, M. Manzañera, M. J. Campos, S. Vichez, and J. L. Ramos. 2002. Cross-regulation between a novel two-component signal transduction system for catabolism of toluene in Pseudomonas mendocina and the TodST system from Pseudomonas putida. J. Bacteriol. 184:7062-7067.[Abstract/Free Full Text]
- 206 Reineke, W. 1998. Development of hybrid strains for the mineralization of chloroaromatics by patchwork assembly. Annu. Rev. Microbiol. 52:287-331.[CrossRef][Medline]
- 207 Reineke, W., and H.-J. Knackmuss. 1988. Microbial degradation of haloaromatics. Annu. Rev. Microbiol. 42:263-287.[CrossRef][Medline]
- 208 Reitzer, L. J., and B. Magasanik. 1986. Transcription of glnA in E. coli is stimulated by activator bound to sites far from the promoter. Cell 45:785-792.[CrossRef][Medline]
- 209 Reizer, J., and M. H. Saier, Jr. 1997. Modular multidomain phosphoryl transfer proteins of bacteria. Curr. Opin. Struct. Biol. 7:407-415.[CrossRef][Medline]
- 210 Rhee, S., R. G. Martin, J. L. Rosner, and D. R. Davies. 1998. A novel DNA- binding motif in MarA: the first structure for an AraC family transcriptional activator. Proc. Natl. Acad. Sci. USA 95:10413-10418.[Abstract/Free Full Text]
- 211 Rigali, S., A. Derouaux, F. Giannotta, and J. Dusart. 2002. Subdivision of the helix-turn-helix GntR family of bacterial regulators in the FadR, HutC, MocR, and YtrA subfamilies. J. Biol. Chem. 277:12507-12515.[Abstract/Free Full Text]
- 212 Roméro-Arroyo, C. E., M. A. Schell, G. L. Gaines, and E. L. Neidle. 1995. catM encodes a LysR-type transcriptional activator regulating catechol degradation in Acinetobacter calcoaceticus. J. Bacteriol. 177:5891-5898.[Abstract/Free Full Text]
- 213 Romero-Steiner, S., R. E. Parales, C. S. Harwood, and J. E. Houghton. 1994. Characterization of the pcaR regulatory gene from Pseudomonas putida, which is required for the complete degradation of p-hydroxybenzoate. J. Bacteriol. 176:5771-5779.[Abstract/Free Full Text]
- 214 Roper, D. I., T. Fawcett, and R. A. Cooper. 1993. The Escherichia coli C homoprotocatechuate degradative operon: hpc gene order, direction of transcription and control of expression. Mol. Gen. Genet. 237:241-250.[Medline]
- 215 Rothmel, R. K., T. L. Aldrich, J. E. Houghton, W. M. Coco, L. N. Ornston, and A. M. Chakrabarty. 1990. Nucleotide sequencing and characterization of Pseudomonas putida catR: a positive regulator of the catBC operon is a member of the LysR family. J. Bacteriol. 172:922-931.[Abstract/Free Full Text]
- 216 Rothmel, R. K., D. L. Shinabarger, M. R. Parsek, T. L. Aldrich, and A. M. Chakrabarty. 1991. Functional analysis of the Pseudomonas putida regulatory protein CatR: transcriptional studies and determination of the CatR DNA-binding site by hydroxyl-radical footprinting. J. Bacteriol. 173:4717-4724.[Abstract/Free Full Text]
- 217 Ruíz, R., S. Marqués, and J. L. Ramos. 2003. Leucines 193 and 194 at the N- terminal domain of the XylS protein, the positive transcriptional regulator of the TOL meta-cleavage pathway, are involved in dimerization. J. Bacteriol. 185:3036-3041.[Abstract/Free Full Text]
- 218 Ruíz, R., and J. L. Ramos. 2002. Residues 137 and 153 at the N terminus of the XylS protein influence the effector profile of this transcriptional regulator and the
factor used by RNA polymerase to stimulate transcription from its cognate promoter. J. Biol. Chem. 277:7282-7286.[Abstract/Free Full Text]
- 219 Ruíz, R., and J. L. Ramos. 2001. Residues 137 and 153 of XylS influence contacts with the C-terminal domain of the RNA polymerase
subunit. Biochem. Biophys. Res. Commun. 287:519-521.[CrossRef][Medline]
- 220 Ruíz, R., J. L. Ramos, and S. M. Egan. 2001. Interactions of the XylS regulators with the C-terminal domain of the RNA polymerase
subunit influence the expression level from the cognate Pm promoter. FEBS Lett. 491:207-211.[CrossRef][Medline]
- 221 Salto, R., A. Delgado, C. Michán, S. Marqués, and J. L. Ramos. 1998. Modulation of the function of the signal receptor domain of XylR, a member of a family of prokaryotic enhancer-like positive regulators. J. Bacteriol. 180:600-604.[Abstract/Free Full Text]
- 222 Santos, P. M., L. Leoni, I. Di Bartolo, and E. Zennaro. 2002. Integration host factor is essential for the optimal expression of the styABCD operon in Pseudomonas fluorescens ST. Res. Microbiol. 153:527-536.[CrossRef][Medline]
- 223 Sasse-Dwight, S., and J. D. Gralla. 1988. Probing the Escherichia coli glnALG upstream activation mechanism in vivo. Proc. Natl. Acad. Sci. USA 85:8934-8938.[Abstract/Free Full Text]
- 224 Schell, M. A. 1993. Molecular biology of the LysR family of transcriptional regulators. Annu. Rev. Microbiol. 47:597-626.[CrossRef][Medline]
- 225 Schell, M. A. 1985. Transcriptional control of the nah and sal hydrocarbon-degradation operons by the nahR gene product. Gene 36:301-309.[CrossRef][Medline]
- 226 Schell, M. A., P. H. Brown, and S. Raju. 1990. Use of saturation mutagenesis to localize probable functional domains in the NahR protein, a LysR-type transcription activator. J. Biol. Chem. 265:3844-3850.[Abstract/Free Full Text]
- 227 Schell, M. A., and E. F. Poser. 1989. Demonstration, characterization, and mutational analysis of NahR protein binding to nah and sal promoters. J. Bacteriol. 171:837-846.[Abstract/Free Full Text]
- 228 Schell, M. A., and P. E. Wender. 1986. Identification of the nahR gene product and nucleotide sequences required for its activation of the sal operon. J. Bacteriol. 166:9-14.[Abstract/Free Full Text]
- 229 Schirmer, F., S. Ehrt, and W. Hillen. 1997. Expression, inducer spectrum, domain structure, and function of MopR, the regulator of phenol degradation in Acinetobacter calcoaceticus NCIB8250. J. Bacteriol. 179:1329-1336.[Abstract/Free Full Text]
- 230 Schoemaker, H. E., D. Mink, and M. G. Wubbolts. 2003. Dispelling the mythsbiocatalysis in industrial synthesis. Science 299:1694-1697.[Abstract/Free Full Text]
- 231 Schumacher, J., X. Zhang, S. Jones, P. Bordes, and M. Buck. 2004. ATP-dependent transcriptional activation by bacterial PspF AAA+ protein. J. Mol. Biol. 338:863-875.[CrossRef][Medline]
- 232 Shingler, V. 2003. Integrated regulation in response to aromatic compounds: from signal sensing to attractive behaviour. Environ. Microbiol. 5:1226-1241.[CrossRef][Medline]
- 233 Shingler, V. 1996. Signal sensing by
54-dependent regulators: derepression as a control mechanism. Mol. Microbiol. 19:409-416.[CrossRef][Medline]
- 234 Shingler, V., M. Bartilson, and T. Moore. 1993. Cloning and nucleotide sequence of the gene encoding the positive regulator (DmpR) of the phenol catabolic pathway encoded by pVI150 and identification of DmpR as a member of the NtrC family of transcriptional activators. J. Bacteriol. 175:1596-1604.[Abstract/Free Full Text]
- 235 Shingler, V., and T. Moore. 1994. Sensing of aromatic compounds by the DmpR transcriptional activator of phenol-catabolizing Pseudomonas sp. strain CF600. J. Bacteriol. 176:1555-1560.[Abstract/Free Full Text]
- 236 Shingler, V., and H. Pavel. 1995. Direct regulation of the ATPase activity of the transcriptional activator DmpR by aromatic compounds. Mol. Microbiol. 17:505-513.[CrossRef][Medline]
- 237 Skarfstad, E., E. O'Neill, J. Garmendia, and V. Shingler. 2000. Identification of an effector specificity subregion within the aromatic-responsive regulators DmpR and XylR by DNA shuffling. J. Bacteriol. 182:3008-3016.[Abstract/Free Full Text]
- 238 Smidt, H., M. van Leest, J. van der Oost, and W. M. de Vos. 2000. Transcriptional regulation of the cpr gene cluster in ortho-chlorophenol-respiring Desulfitobacterium dehalogenans. J. Bacteriol. 182:5683-5691.[Abstract/Free Full Text]
- 239 Soisson, S. M., B. MacDougall-Shackleton, R. Schleif, and C. Wolberger. 1997. Structural basis for ligand-regulated oligomerization of AraC. Science 276:421-425.[Abstract/Free Full Text]
- 240 Spain, J. 1997. Synthetic chemicals with potential for natural attenuation. Bioremed. J. 1:1-9.
- 241 Spooner, R. A., M. Bagdasarian, and F. C. Franklin. 1987. Activation of the xylDLEGF promoter of the TOL toluene-xylene degradation pathway by overproduction of the xylS regulatory gene product. J. Bacteriol. 169:3581-3586.[Abstract/Free Full Text]
- 242 Sticher, P., M. C. M. Jaspers, K. Stemmler, H. Harms, A. J. B. Zehnder, and J. R. van der Meer. 1997. Development and characterization of a whole-cell bioluminescent sensor for bioavailable middle-chain alkanes in contaminated groundwater samples. Appl. Environ. Microbiol. 63:4053-4060.[Abstract]
- 243 Stock, A. M., V. L. Robinson, and P. N. Goudreau. 2000. Two-component signal transduction. Annu. Rev. Biochem. 69:183-215.[CrossRef][Medline]
- 244 Reference deleted.
- 245 Sunnarborg, A., D. Klumpp, T. Chung, and D. C. LaPorte. 1990. Regulation of the glyoxylate bypass operon: cloning and characterization of iclR. J. Bacteriol. 172:2642-2649.[Abstract/Free Full Text]
- 246 Suzuki, K., N. Ogawa, and K. Miyashita. 2001. Expression of 2-halobenzoate dioxygenase genes (cbdSABC) involved in the degradation of benzoate and 2-halobenzoate in Burkholderia sp. TH2. Gene 262:137-145.[CrossRef][Medline]
- 247 Sze, C. C., A. D. Laurie, and V. Shingler. 2001. In vivo and in vitro effects of integration host factor at the DmpR-regulated
54-dependent Po promoter. J. Bacteriol. 183:2842-2851.[Abstract/Free Full Text]
- 248 Taylor, B. L., and I. B. Zhulin. 1999. PAS domains: internal sensors of oxygen, redox potential, and light. Microbiol. Mol. Biol. Rev. 63:479-506.[Abstract/Free Full Text]
- 249 Teramoto, M., S. Harayama, and K. Watanabe. 2001. PhcS represses gratuitous expression of phenol-metabolizing enzymes in Comamonas testosteroni R5. J. Bacteriol. 183:4227-4234.[Abstract/Free Full Text]
- 250 Teramoto, M., K. Ohnishi, S. Harayama, and K. Watanabe. 2002. An AraC/XylS family member at a high level in a hierarchy of regulators for phenol-metabolizing enzymes in Comamonas testosteroni R5. J. Bacteriol. 184:3941-3946.[Abstract/Free Full Text]
- 251 Tobes, R., and J. L. Ramos. 2002. AraC-XylS database: a family of positive transcriptional regulators in bacteria. Nucleic Acids Res. 30:318-321.[Abstract/Free Full Text]
- 252 Torres, B., G. Porras, J. L. García, and E. Díaz. 2003. Regulation of the mhp cluster responsible for 3-(3-hydroxyphenyl)propionic acid degradation in Escherichia coli. J. Biol. Chem. 278:27575-27585.[Abstract/Free Full Text]
- 253 Tralau, T., J. Mampel, A. M. Cook, and J. Ruff. 2003. Characterization of TsaR, an oxygen-sensitive LysR-type regulator for the degradation of p-toluenesulfonate in Comamonas testosteroni T-2. Appl. Environ. Microbiol. 69:2298-2305.[Abstract/Free Full Text]
- 254 Trautwein, G., and U. Gerischer. 2001. Effects exerted by transcriptional regulator PcaU from Acinetobacter sp. strain ADP1. J. Bacteriol. 183:873-881.[Abstract/Free Full Text]
- 255 Tropel, D., and J. R. van der Meer. 2002. Identification and physical characterization of the HbpR binding sites of the hbpC and hbpD promoters. J. Bacteriol. 184:2914-2924.[Abstract/Free Full Text]
- 256 Tsoi, T. V., E. G. Plotnikova, J. R. Cole, W. F. Guerin, M. Bagdasarian, and J. M. Tiedje. 1999. Cloning, expression, and nucleotide sequence of the Pseudomonas aeruginosa 142 ohb genes coding for oxygenolytic ortho dehalogenation of halobenzoates. Appl. Environ. Microbiol. 65:2151-2162.[Abstract/Free Full Text]
- 257 Turner, R., and R. Tjian. 1989. Leucine repeats and an adjacent DNA binding domain mediate the formation of functional cFos-cJun heterodimers. Science 243:1689-1694.[Abstract/Free Full Text]
- 258 Valls, M., and V. de Lorenzo. 2003. Transient XylR binding to the UAS of the Pseudomonas putida
54 promoter Pu revealed with high intensity UV footprinting in vivo. Nucleic Acids Res. 31:6926-6934.[Abstract/Free Full Text]
- 259 van Aalten, D. M., C. C. DiRusso, and J. Knudsen. 2001. The structural basis of acyl coenzyme A-dependent regulation of the transcription factor FadR. EMBO J. 20:2041-2050.[CrossRef][Medline]
- 260 van Aalten, D. M., C. C. DiRusso, J. Knudsen, and R. K. Wierenga. 2000. Crystal structure of FadR, a fatty acid-responsive transcription factor with a novel acyl coenzyme A-binding fold. EMBO J. 19:5167-5177.[CrossRef][Medline]
- 261 van der Meer, J. R. 1997. Evolution of novel metabolic pathways for the degradation of chloroaromatic compounds. Antonie Leeuwenhoek 71:159-178.[CrossRef][Medline]
- 262 van der Meer, J. R., W. M. de Vos, S. Harayama, and A. J. B. Zehnder. 1992. Molecular mechanisms of genetic adaptation to xenobiotic compounds. Microbiol. Rev. 56:677-694.[Abstract/Free Full Text]
- 263 van der Meer, J. R., A. C. Frijters, J. H. J. Leveau, R. I. L. Eggen, A. J. B. Zehnder, and W. M. de Vos. 1991. Characterization of the Pseudomonas sp. strain P51 gene tcbR, a LysR-type transcriptional activator of the tcbCDEF chlorocatechol oxidative operon, and analysis of the regulatory region. J. Bacteriol. 173:3700-3708.[Abstract/Free Full Text]
- 264 Velasco, A., S. Alonso, J. L. García, J. Perera, and E. Díaz. 1998. Genetic and functional analysis of the styrene catabolic cluster of Pseudomonas sp. strain Y2. J. Bacteriol. 180:1063-1071.[Abstract/Free Full Text]
- 265 Vicente, M., K. F. Chater, and V. De Lorenzo. 1999. Bacterial transcription factors involved in global regulation. Mol. Microbiol. 33:8-17.[CrossRef][Medline]
- 266 Volz, K. 1993. Structural conservation in the CheY superfamily. Biochemistry 32:11741-11753.[CrossRef][Medline]
- 267 Wang, Y. K., J. H. Lee, J. M. Brewer, and T. R. Hoover. 1997. A conserved region in the
54-dependent activator DctD is involved in both binding to RNA polymerase and coupling ATP hydrolysis to activation. Mol. Microbiol. 26:373-386.[CrossRef][Medline]
- 268 Watanabe, T., H. Fujihara, and K. Furukawa. 2003. Characterization of the second LysR-type regulator in the biphenyl-catabolic gene cluster of Pseudomonas pseudoalcaligenes KF707. J. Bacteriol. 185:3575-3582.[Abstract/Free Full Text]
- 269 Watanabe, T., R. Inoue, N. Kimura, and K. Furukawa. 2000. Versatile transcription of biphenyl catabolic bph operon in Pseudomonas pseudoalcaligenes KF707. J. Biol. Chem. 275:31016-31023.[Abstract/Free Full Text]
- 270 Wikström, P., E. O'Neill, L. C. Ng, and V. Shingler. 2001. The regulatory N- terminal region of the aromatic-responsive transcriptional activator DmpR constrains nucleotide-triggered multimerisation. J. Mol. Biol. 314:971-984.[CrossRef][Medline]
- 271 Williams, P. A., and J. R. Sayers. 1994. The evolution of pathways for aromatic hydrocarbon oxidation in Pseudomonas. Biodegradation 5:195-217.[CrossRef][Medline]
- 272 Wu, R. Y., R. G. Zhang, O. Zagnitko, I. Dementieva, N. Maltzev, J. D. Watson, R. Laskowski, P. Gornicki, and A. Joachimiak. 2003. Crystal structure of Enterococcus faecalis SlyA-like transcriptional factor. J. Biol. Chem. 278:20240-20244.[Abstract/Free Full Text]
- 273 Xu, Y., R. J. Heath, Z. Li, C. O. Rock, and S. W. White. 2001. The FadR-DNA complex. Transcriptional control of fatty acid metabolism in Escherichia coli. J. Biol. Chem. 276:17373-17379.[Abstract/Free Full Text]
- 274 Yen, K. M., and I. C. Gunsalus. 1985. Regulation of naphthalene catabolic genes of plasmid NAH7. J. Bacteriol. 162:1008-1013.[Abstract/Free Full Text]
- 275 Zhang, R. G., Y. Kim, T. Skarina, S. Beasley, R. Laskowski, C. Arrowsmith, A. Edwards, A. Joachimiak, and A. Savchenko. 2002. Crystal structure of Thermotoga maritima 0065, a member of the IclR transcriptional factor family. J. Biol. Chem. 277:19183-19190.[Abstract/Free Full Text]
- 276 Zhulin, I. B., B. L. Taylor, and R. Dixon. 1997. PAS domain S-boxes in Archaea, Bacteria and sensors for oxygen and redox. Trends Biochem. Sci. 22:331-333.[CrossRef][Medline]
Microbiology and Molecular Biology Reviews, September 2004, p. 474-500, Vol. 68, No. 3
1092-2172/04/$08.00+0 DOI: 10.1128/MMBR.68.3.474-500.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.
This article has been cited by other articles:
-
Mustakhimov, I. I., Reshetnikov, A. S., Glukhov, A. S., Khmelenina, V. N., Kalyuzhnaya, M. G., Trotsenko, Y. A.
(2010). Identification and Characterization of EctR1, a New Transcriptional Regulator of the Ectoine Biosynthesis Genes in the Halotolerant Methanotroph Methylomicrobium alcaliphilum 20Z. J. Bacteriol.
192: 410-417
[Abstract]
[Full Text]
-
Yagi, J. M., Madsen, E. L.
(2009). Diversity, Abundance, and Consistency of Microbial Oxygenase Expression and Biodegradation in a Shallow Contaminated Aquifer. Appl. Environ. Microbiol.
75: 6478-6487
[Abstract]
[Full Text]
-
Camara, B., Nikodem, P., Bielecki, P., Bobadilla, R., Junca, H., Pieper, D. H.
(2009). Characterization of a Gene Cluster Involved in 4-Chlorocatechol Degradation by Pseudomonas reinekei MT1. J. Bacteriol.
191: 4905-4915
[Abstract]
[Full Text]
-
Schleinitz, K. M., Schmeling, S., Jehmlich, N., von Bergen, M., Harms, H., Kleinsteuber, S., Vogt, C., Fuchs, G.
(2009). Phenol Degradation in the Strictly Anaerobic Iron-Reducing Bacterium Geobacter metallireducens GS-15. Appl. Environ. Microbiol.
75: 3912-3919
[Abstract]
[Full Text]
-
Shin, K. A., Spain, J. C.
(2009). Pathway and Evolutionary Implications of Diphenylamine Biodegradation by Burkholderia sp. Strain JS667. Appl. Environ. Microbiol.
75: 2694-2704
[Abstract]
[Full Text]
-
Chai, Y., Kolter, R., Losick, R.
(2009). A Widely Conserved Gene Cluster Required for Lactate Utilization in Bacillus subtilis and Its Involvement in Biofilm Formation. J. Bacteriol.
191: 2423-2430
[Abstract]
[Full Text]
-
Carmona, M., Zamarro, M. T., Blazquez, B., Durante-Rodriguez, G., Juarez, J. F., Valderrama, J. A., Barragan, M. J. L., Garcia, J. L., Diaz, E.
(2009). Anaerobic Catabolism of Aromatic Compounds: a Genetic and Genomic View. Microbiol. Mol. Biol. Rev.
73: 71-133
[Abstract]
[Full Text]
-
Pope, S. D., Chen, L.-L., Stewart, V.
(2009). Purine Utilization by Klebsiella oxytoca M5al: Genes for Ring-Oxidizing and -Opening Enzymes. J. Bacteriol.
191: 1006-1017
[Abstract]
[Full Text]
-
Iida, T., Waki, T., Nakamura, K., Mukouzaka, Y., Kudo, T.
(2009). The GAF-Like-Domain-Containing Transcriptional Regulator DfdR Is a Sensor Protein for Dibenzofuran and Several Hydrophobic Aromatic Compounds. J. Bacteriol.
191: 123-134
[Abstract]
[Full Text]
-
Carbajosa, G., Trigo, A., Valencia, A., Cases, I.
(2009). Bionemo: molecular information on biodegradation metabolism. Nucleic Acids Res
37: D598-D602
[Abstract]
[Full Text]
-
Maddocks, S. E., Oyston, P. C. F.
(2008). Structure and function of the LysR-type transcriptional regulator (LTTR) family proteins. Microbiology
154: 3609-3623
[Abstract]
[Full Text]
-
Jerg, B., Gerischer, U.
(2008). Relevance of nucleotides of the PcaU binding site from Acinetobacter baylyi. Microbiology
154: 756-766
[Abstract]
[Full Text]
-
Durante-Rodriguez, G., Zamarro, M. T., Garcia, J. L., Diaz, E., Carmona, M.
(2008). New insights into the BzdR-mediated transcriptional regulation of the anaerobic catabolism of benzoate in Azoarcus sp. CIB. Microbiology
154: 306-316
[Abstract]
[Full Text]
-
Thanbichler, M., Iniesta, A. A., Shapiro, L.
(2007). A comprehensive set of plasmids for vanillate- and xylose-inducible gene expression in Caulobacter crescentus. Nucleic Acids Res
35: e137-e137
[Abstract]
[Full Text]
-
Martinez-Perez, O., Lopez-Sanchez, A., Reyes-Ramirez, F., Floriano, B., Santero, E.
(2007). Integrated Response to Inducers by Communication between a Catabolic Pathway and Its Regulatory System. J. Bacteriol.
189: 3768-3775
[Abstract]
[Full Text]
-
Choi, K. Y., Zylstra, G. J., Kim, E.
(2007). Benzoate Catabolite Repression of the Phthalate Degradation Pathway in Rhodococcus sp. Strain DK17. Appl. Environ. Microbiol.
73: 1370-1374
[Abstract]
[Full Text]
-
Siehler, S. Y., Dal, S., Fischer, R., Patz, P., Gerischer, U.
(2007). Multiple-Level Regulation of Genes for Protocatechuate Degradation in Acinetobacter baylyi Includes Cross-Regulation. Appl. Environ. Microbiol.
73: 232-242
[Abstract]
[Full Text]
-
Goller, C., Wang, X., Itoh, Y., Romeo, T.
(2006). The Cation-Responsive Protein NhaR of Escherichia coli Activates pgaABCD Transcription, Required for Production of the Biofilm Adhesin Poly-{beta}-1,6-N-Acetyl-D-Glucosamine. J. Bacteriol.
188: 8022-8032
[Abstract]
[Full Text]
-
Alhapel, A., Darley, D. J., Wagener, N., Eckel, E., Elsner, N., Pierik, A. J.
(2006). Molecular and functional analysis of nicotinate catabolism in Eubacterium barkeri. Proc. Natl. Acad. Sci. USA
103: 12341-12346
[Abstract]
[Full Text]
-
Kouzuma, A., Pinyakong, O., Nojiri, H., Omori, T., Yamane, H., Habe, H.
(2006). Functional and transcriptional analyses of the initial oxygenase genes for acenaphthene degradation from Sphingomonas sp. strain A4.. Microbiology
152: 2455-2467
[Abstract]
[Full Text]
-
Fujihara, H., Yoshida, H., Matsunaga, T., Goto, M., Furukawa, K.
(2006). Cross-Regulation of Biphenyl- and Salicylate-Catabolic Genes by Two Regulatory Systems in Pseudomonas pseudoalcaligenes KF707. J. Bacteriol.
188: 4690-4697
[Abstract]
[Full Text]
-
del Peso-Santos, T., Bartolome-Martin, D., Fernandez, C., Alonso, S., Garcia, J. L., Diaz, E., Shingler, V., Perera, J.
(2006). Coregulation by Phenylacetyl-Coenzyme A-Responsive PaaX Integrates Control of the Upper and Lower Pathways for Catabolism of Styrene by Pseudomonas sp. Strain Y2. J. Bacteriol.
188: 4812-4821
[Abstract]
[Full Text]
-
Lacal, J., Busch, A., Guazzaroni, M.-E., Krell, T., Ramos, J. L.
(2006). The TodS-TodT two-component regulatory system recognizes a wide range of effectors and works with DNA-bending proteins. Proc. Natl. Acad. Sci. USA
103: 8191-8196
[Abstract]
[Full Text]
-
Miyakoshi, M., Urata, M., Habe, H., Omori, T., Yamane, H., Nojiri, H.
(2006). Differentiation of Carbazole Catabolic Operons by Replacement of the Regulated Promoter via Transposition of an Insertion Sequence. J. Biol. Chem.
281: 8450-8457
[Abstract]
[Full Text]
-
Ezezika, O. C., Collier-Hyams, L. S., Dale, H. A., Burk, A. C., Neidle, E. L.
(2006). CatM Regulation of the benABCDE Operon: Functional Divergence of Two LysR-Type Paralogs in Acinetobacter baylyi ADP1.. Appl. Environ. Microbiol.
72: 1749-1758
[Abstract]
[Full Text]
-
Arias-Barrau, E., Sandoval, A., Naharro, G., Olivera, E. R., Luengo, J. M.
(2005). A Two-component Hydroxylase Involved in the Assimilation of 3-Hydroxyphenyl Acetate in Pseudomonas putida. J. Biol. Chem.
280: 26435-26447
[Abstract]
[Full Text]
-
Shen, X.-H., Jiang, C.-Y., Huang, Y., Liu, Z.-P., Liu, S.-J.
(2005). Functional Identification of Novel Genes Involved in the Glutathione-Independent Gentisate Pathway in Corynebacterium glutamicum. Appl. Environ. Microbiol.
71: 3442-3452
[Abstract]
[Full Text]
-
Patrauchan, M. A., Florizone, C., Dosanjh, M., Mohn, W. W., Davies, J., Eltis, L. D.
(2005). Catabolism of Benzoate and Phthalate in Rhodococcus sp. Strain RHA1: Redundancies and Convergence. J. Bacteriol.
187: 4050-4063
[Abstract]
[Full Text]
-
Ramos, J. L., Martinez-Bueno, M., Molina-Henares, A. J., Teran, W., Watanabe, K., Zhang, X., Gallegos, M. T., Brennan, R., Tobes, R.
(2005). The TetR Family of Transcriptional Repressors. Microbiol. Mol. Biol. Rev.
69: 326-356
[Abstract]
[Full Text]