Visualization of DNA-protein intermediates during activation of the Pu promoter of the TOL plasmid of Pseudomonas putida

Characterisation of the putative effector interaction site of the regulatory HbpR protein from Pseudomonas azelaica by site-directed mutagenesis

Bacterial transcription activators of the XylR/DmpR subfamily exert their expression control via σ(54)-dependent RNA polymerase upon stimulation by a chemical effector, typically an aromatic compound. Where the chemical effector interacts with the transcription regulator protein to achieve activation is still largely unknown. Here we focus on the HbpR protein from Pseudomonas azelaica, which is a member of the XylR/DmpR subfamily and responds to biaromatic effectors such as 2-hydroxybiphenyl. We use protein structure modeling to predict folding of the effector recognition domain of HbpR and molecular docking to identify the region where 2-hydroxybiphenyl may interact with HbpR. A large number of site-directed HbpR mutants of residues in- and outside the predicted interaction area was created and their potential to induce reporter gene expression in Escherichia coli from the cognate P(C) promoter upon activation with 2-hydroxybiphenyl was studied. Mutant proteins were purified to study their conformation. Critical residues for effector stimulation indeed grouped near the predicted area, some of which are conserved among XylR/DmpR subfamily members in spite of displaying different effector specificities. This suggests that they are important for the process of effector activation, but not necessarily for effector specificity recognition.

Transcriptional wiring of the TOL plasmid regulatory network to its host involves the submission of the sigma54-promoter Pu to the response regulator PprA

Implantation of the regulatory circuit of the degradation pathway of TOL plasmid pWW0 in the native transcriptional network of the host Pseudomonas putida involves interplay between plasmid- and chromosome-encoded factors. We have employed a reverse genetics approach to investigate such a molecular wiring by identifying host proteins that form stable complexes with Pu, the sigma(54)-dependent promoter of the upper TOL operon of pWW0. This approach revealed that the Pu upstream activating sequences (UAS), the target sites of the cognate activator XylR, form a specific complex with a host protein which, following DNA affinity purification and mass spectrometry analysis, was identified as the LytTR-type two-component response regulator PprA. Directed inactivation of pprA resulted in the upregulation of the Pu promoter in vivo, while expression of the same gene from a plasmid vector strongly repressed Pu activity. Such a downregulation of Pu by PprA could be faithfully reproduced both in vitro with purified components and in an in vivo reporter system assembled in Escherichia coli. The overlap of the PprA and XylR binding sites suggested that the basis for the inhibitory effect on Pu was a mutual exclusion mechanism between the two proteins to bind the UAS. We argue that the binding of the response regulator PprA to Pu (a case without precedents in sigma(54)-dependent transcription) helps to anchor the TOL regulatory subnetwork to the wider context of the host transcriptome, thereby allowing the entry of physiological signals that modulate the outcome of promoter activity.

In vivo drafting of single-chain antibodies for regulatory duty on the sigma54-promoter Pu of the TOL plasmid

The identification of single-chain antibodies (scFvs) that interfere in vivo with the building of the complex that activate the prokaryotic, sigma54-dependent promoter Pu of the catabolic TOL plasmid pWW0 is reported. To this end, a phage M13 library of scFvs was raised against the cognate prokaryotic enhancer-binding activator, XylR. The scFv pool was then expressed intracellularly in a reporter Pu-lacZ strain of Escherichia coli designed to permit formation of intramolecular disulphide bonds in cytoplasmic proteins. This strain allowed the assembly of functional scFvs and the direct testing of their activity on the Pu promoter in vivo. Specifically, genetic screening for lacZ-minus colonies yielded a number of scFvs able to downregulate transcriptional output in live cells. Two antibody clones were purified and shown to inhibit the activity of the same promoter in vitro as well. These scFvs targeted the DNA-binding domain of XylR and its ATP binding site respectively. This work provides a proof of principle that mimetic regulatory factors can be derived from an antibody repertoire that specifically interact with given transcriptional activators. As assembly of initiation complexes is stimulated or inhibited by regulatory proteins we argue that anti-XylR scFvs operate as bona fide transcriptional inhibitors of the Pu promoter.

The upstream-activating sequences of the sigma54 promoter Pu of Pseudomonas putida filter transcription readthrough from upstream genes

Although the m-xylene-responsive sigma54 promoter Pu of Pseudomonas putida mt-2, borne by the TOL plasmid pWWO, is one of the strongest known promoters in vivo, its base-line level in the absence of its aromatic inducer is below the limit of any detection procedure. This is unusual because regulatory networks (such as the one to which Pu belongs) can hardly escape the noise caused by intrinsic fluctuations in background transcription, including that transmitted from upstream promoters. This study provides genetic evidence that the upstream-activating sequences (UAS), which serve as the binding sites for the pWW0-encoded XylR protein (the m-xylene-responsive sigma54-dependent activator of Pu), isolate expression of the upper TOL genes from any adventitious transcriptional flow originating further upstream. An in vivo test system was developed in which different segments of the Pu promoter were examined for the inhibition of incoming transcription products from an upstream promoter in P. putida and Escherichia coli. Minimal transcription filter ability was located within a 105-bp fragment encompassing the UAS of Pu. Although S1 nuclease assays showed that the UAS prevented the buildup of downstream transcripts, the mechanism seems to diverge from a typical termination system. This was shown by the fact that the UAS did not halt transcription in vitro and that the filter effect could not be relieved by the anti-termination system of lambda phage. Because the Pu promoter lies adjacent to the edge of a transposon in pWW0, the preset transcriptional filter in the UAS may isolate the upper TOL operon from undue expression after random insertion of the mobile genetic element in a new replicon.

Characterization of HbpR binding by site-directed mutagenesis of its DNA-binding site and by deletion of the effector domain

In the presence of 2-hydroxybiphenyl, the enhancer binding protein, HbpR, activates the sigma54-dependent P(hbpC) promoter and controls the initial steps of 2-hydroxybiphenyl degradation in Pseudomonas azelaica. In the activation process, an oligomeric HbpR complex of unknown subunit composition binds to an operator region containing two imperfect palindromic sequences. Here, the HbpR-DNA binding interactions were investigated by site-directed mutagenesis of the operator region and by DNA-binding assays using purified HbpR. Mutations that disrupted the twofold symmetry in the palindromes did not affect the binding affinity of HbpR, but various mutations along a 60 bp region, and also outside the direct palindromic sequences, decreased the binding affinity. Footprints of HbpR on mutant operator fragments showed that a partial loss of binding contacts occurs, suggesting that the binding of one HbpR 'protomer' in the oligomeric complex is impaired whilst leaving the other contacts intact. An HbpR variant, devoid of its N-terminal sensing A-domain, was unable to activate transcription from the hbpC promoter while maintaining protection of the operator DNA in footprints. Wild-type HbpR was unable to activate transcription from the hbpC promoter when delta A-HbpR was expressed in the same cell, suggesting the formation of (repressing) hetero-oligomers. This model implies that HbpR can self-associate on its operator DNA without effector recognition or ATP binding. Furthermore, our findings suggest that the N-terminal sensing domain of HbpR is needed to activate the central ATPase domain rather than to repress a constitutively active C domain, as is the case for the related regulatory protein XylR.

Construction and comparison of Escherichia coli whole-cell biosensors capable of detecting aromatic compounds

The XylR regulatory protein is a transcription factor involved in the BTEX (benzene, toluene, ethylbenzene, and xylene) degradation pathway in Pseudomonas species. When XylR-dependent stimulation of transcription from a plasmid containing XylR and its cognate promoters Pr and Pu was monitored as firefly luciferase activities in Escherichia coli, a notably high level of basal activity was observed in the absence of inducers. To improve the response specificity of XylR in this system, two related but different promoters were tested for their activities; the XylS activator promoter Ps and the DmpR activator promoter Po. Po with the deletion of its own upstream activating sequences (UASs; Po') showed a very low level of basal activity compared to Pu and Ps. The maximum level with the addition of inducers was increased 3151-fold by o-xylene with Po', while it was 31.5 and 74.1 fold by m-xylene with Pu and Ps, respectively. Gel mobility shift assay showed that the purified XylR without inducers can bind to Pr/Pu but not to Pr/Po', implying that XylR multimerization with Pr/Pu could be formed for initiation of transcription in this system. The data suggest that Po' can be an excellent alternative in constructing a signal-intensified, whole-cell biosensor in response to the xenobiotics.

Transient XylR binding to the UAS of the Pseudomonas putida sigma54 promoter Pu revealed with high intensity UV footprinting in vivo

The binding of the transcriptional regulator XylR to its cognate upstream activating sequences (UAS) of the sigma54-dependent promoter Pu of Pseudomonas putida has been examined in vivo in single copy gene dose and stoichiometry. To this end, we have employed a novel in vivo genomic footprinting procedure that uses short exposures of bacterial cells to diffuse high intensity UV light that causes formation of TT or TC dimers. In contrast to simpler models for activation of sigma54-dependent promoters, our results clearly indicate that the XylR protein is not permanently bound in vivo to its target sites in Pu. On the contrary, the UAS appear to be mostly unoccupied at all growth stages. This is in contrast to the integration host factor (IHF), which binds Pu strongly in vivo at stationary phase, as also revealed by UV footprinting. Only overexpression of XylR altered the photoreactivity of the corresponding DNA region to report stable binding of the regulator to the UAS. However, the presence of aromatic XylR inducers reversed the forced occupation caused by increased levels of the activator. These results are compatible with the notion that XylR interacts very transiently with the UAS and detaches from the promoter during transcriptional activation of Pu.

The C-terminal domain of Eos forms a high order complex in solution

Ikaros family transcription factors play important roles in the control of hematopoiesis. Family members are predicted to contain up to six classic zinc fingers that are arranged into N- and C-terminal domains. The N-terminal domain is responsible for site-specific DNA binding, whereas the C-terminal domain primarily mediates the homo- and hetero-oligomerization between family members. Although the mechanisms of action of these proteins are not completely understood, the zinc finger domains are known to play a central role. In the current study, we have sought to understand the physical and functional properties of these domains, in particular the C-terminal domain. We show that the N-terminal domain from Eos, and not its C-terminal region, is required to recognize GGGA consensus sequences. Surprisingly, in contrast to the behavior exhibited by Ikaros, the C-terminal domain of Eos inhibits the DNA-binding activity of the full-length protein. In addition, we have used a range of biophysical techniques to demonstrate that the C-terminal domain of Eos mediates the formation of complexes that consist of nine or ten molecules. These results constitute the first direct demonstration that Ikaros family proteins can form higher order complexes in solution, and we discuss this unexpected result in the context of what is currently known about the family members and their possible mechanism of action.

The central domain of Escherichia coli TyrR is responsible for hexamerization associated with tyrosine-mediated repression of gene expression

TyrR from Escherichia coli regulates the expression of genes for aromatic amino acid uptake and biosynthesis. Its central ATP-hydrolyzing domain is similar to conserved domains of bacterial regulatory proteins that interact with RNA polymerase holoenzyme associated with the alternative sigma factor, sigma(54). It is also related to the common module of the AAA+ superfamily of proteins that is involved in a wide range of cellular activities. We expressed and purified two TyrR central domain polypeptides. The fragment comprising residues 188-467, called TyrR-(188-467), was soluble and stable, in contrast to that corresponding to the conserved core from residues 193 to 433. TyrR-(188-467) bound ATP and rhodamine-ATP with association constants 2- to 5-fold lower than TyrR and hydrolyzed ATP at five times the rate of TyrR. In contrast to TyrR, which is predominantly dimeric at protein concentrations less than 10 microm in the absence of ligands, or in the presence of ATP or tyrosine alone, TyrR-(188-467) is a monomer, even at high protein concentrations. Tyrosine in the presence of ATP or ATPgammaS promotes the oligomerization of TyrR-(188-467) to a hexamer. Tyrosine-dependent repression of gene transcription by TyrR therefore depends on ligand binding and hexamerization determinants located in the central domain polypeptide TyrR-(188-467).

Identification and physical characterization of the HbpR binding sites of the hbpC and hbpD promoters

Pseudomonas azelaica HBP1 can use 2-hydroxybiphenyl (2-HBP) and 2,2'-dihydroxybiphenyl as sole carbon and energy sources by means of the hbp regulon. This regulon is composed of three genes, hbpCA and hbpD, coding for enzymes of a meta-cleavage pathway and the hbpR gene, which codes for a XylR/DmpR-type transcription regulator. It was previously shown that HbpR activates transcription from two sigma(54)-dependent promoters, P(hbpC) and P(hbpD), in the presence of 2-HBP. In this study, by using gel mobility shift assays with a purified fusion protein containing calmodulin binding protein (CBP) and HbpR, we detected two binding regions for HbpR in P(hbpC) and one binding region in P(hbpD). DNase I footprints of the proximal binding region of P(hbpC) and of the binding region in P(hbpD) showed that CBP-HbpR protected a region composed of two inverted repeat sequences which were homologous to the binding sites identified for XylR. Unlike the situation in the XylR/P(u) system, we observed simultaneous binding of CBP-HbpR on the two upstream activating sequences (UASs). Fragments with only one UAS did not show an interaction with HbpR, indicating that both pairs of UASs are needed for HbpR binding. The addition of both ATP and 2-HBP increased the DNA binding affinity of HbpR. These results showed for the first time that, for regulators of the XylR/DmpR type, the effector positively affects the recruitment of the regulatory protein on the enhancer DNA.

Monitoring intracellular levels of XylR in Pseudomonas putida with a single-chain antibody specific for aromatic-responsive enhancer-binding proteins

We have isolated a recombinant phage antibody (Phab) that binds a distinct epitope of the subclass of the sigma(54)-dependent prokaryotic enhancer-binding proteins that respond directly to aromatic effectors, e.g., those that activate biodegradative operons of Pseudomonas spp. The DNA segments encoding the variable (V) domains of the immunoglobulins expressed by mice immunized with the C-terminal half of TouR (TouRDeltaA) of Pseudomonas stutzeri OX1 were amplified and rearranged in vitro as single-chain Fv (scFv) genes. An scFv library was thereby constructed, expressed in an M13 display system, and subjected to a panning procedure with TouR. One clone (named B7) was selected with high affinity for TouR and XylR (the regulator of the upper TOL operon of the pWW0 plasmid). The epitope recognized by this Phab was mapped to the peptide TPRAQATLLRVL, which seems to be characteristic of the group of enhancer-binding proteins to which TouR and XylR belong and which is located adjacent to the Walker B motif of the proteins. The Phab B7 was instrumental in measuring directly the intracellular levels of XylR expressed from its natural promoter in monocopy gene dosage in Pseudomonas putida under various conditions. Growth stage, the physical form of the protein produced (XylR or XylRDeltaA), and the presence or absence of aromatic inducers in the medium influenced the intracellular pool of these molecules. XylR oscillated from a minimum of approximately 30 molecules (monomers) per cell during exponential phase to approximately140 molecules per cell at stationary phase. Activation of XylR by aromatic inducers decreased the intracellular concentration of the regulator. The levels of the constitutively active variant of XylR named XylRDeltaA were higher, fluctuating between approximately 90 and approximately 570 molecules per cell, depending on the growth stage. These results are compatible with the present model of transcriptional autoregulation of XylR and suggest the existence of mechanisms controlling the stability of XylR protein in vivo.