Most bacteria control oxidative stress through the H2O2-responsive transactivator OxyR, a member of the LTTR family (LysR Type Transcriptional Regulators), which activates the expression of defensive genes such as those encoding catalases, alkyl hydroperoxide reductases and superoxide dismutases. In the human opportunistic pathogen Pseudomonas aeruginosa, OxyR positively regulates expression of the oxidative stress response genes katA, katB, ahpB and ahpCF. To identify additional targets of OxyR in P. aeruginosa PAO1, we performed chromatin immunoprecipitation in combination with whole genome tiling array analyses (ChIP-chip). We detected 56 genes including all the previously identified defensive genes and a battery of novel direct targets of OxyR. Electrophoretic mobility shift assays (EMSAs) for selected newly identified targets indicated that ∼70% of those were bound by purified oxidized OxyR and their regulation was confirmed by quantitative real-time polymerase chain reaction. Furthermore, a thioredoxin system was identified to enzymatically reduce OxyR under oxidative stress. Functional classification analysis showed that OxyR controls a core regulon of oxidative stress defensive genes, and other genes involved in regulation of iron homeostasis (pvdS), quorum-sensing (rsaL), protein synthesis (rpsL) and oxidative phosphorylation (cyoA and snr1). Collectively, our results indicate that OxyR is involved in oxidative stress defense and regulates other aspects of cellular metabolism as well.

We have demonstrated previously that the chemokine receptors CCR2 and CCR5 form homo-and heterodimers and that dimers can only bind a single chemokine molecule with high affinity. We provide here evidence from bioluminescence resonance energy transfer experiments that stimulation by chemokines does not influence the CCR2/CCR5 heterodimerization status. In addition, we show that the rate of radioligand dissociation from one unit of the heterodimer in "infinite" tracer dilution conditions is strongly increased in the presence of an unlabeled chemokine ligand of the other unit. These results demonstrate unambiguously that the interaction between heterodimer units is of allosteric nature. Agonists, but also some monoclonal antibodies, could promote such negative binding cooperativity, indicating that this phenomenon does not require the full conformational change associated with receptor activation. Finally, we show that G protein coupling is required for high-affinity binding of macrophage inflammatory protein-1␤ (CCL4) to CCR5 and that the dissociation from G proteins, after incubation with Gpp(NH)p, promotes the release of prebound radiolabeled chemokines with kinetics similar to those measured after the addition of an excess of unlabeled chemokines. These observations suggest that the association with G proteins probably participates in the negative cooperativity observed between receptor monomers. We propose that negative cooperativity within homo-and heterodimers of chemokine receptors and probably other G protein-coupled receptors will probably have major implications in their pharmacology in vivo and in the physiopathology of the diseases with which they are associated.The chemokine receptors CCR5 and CCR2 are closely related members of class 1 G protein-coupled receptors (GPCRs). They share 75% overall identity, but most differences are located within the extracellular domains and the C-terminal tail, and this percentage goes up to 91% when considering transmembrane segments only. Yet the pharmacology of the two receptors is clearly different. CCR5 binds MIP-1␣ (CCL3), MIP-1␤ (CCL4), RANTES (CCL5), MCP-2 (CCL8), and a truncated form of hemofiltrate CC chemokine-1 (CCL14) with high affinity , whereas CCR2 binds MCP-1 (CCL2) and MCP-2 (which is thus shared by the two receptors). The ligand binding specificity of these two receptors has been mapped to the extracellular domains, particularly the second extracellular loop, in agreement with the sequence variability found in these regions (Samson et al., 1997). In addition to its role as a chemokine receptor involved in the recruitment of leukocytes in a number of pathological situations (rheumatoid arthritis, graft rejection, neurodegenerative diseases, etc.), CCR5 also constitutes the major coreceptor for macrophage-tropic strains of human immunodeficiency virus, which allows, together with CD4, binding of the viral particles to the cell surface through its envelope protein gp120, triggering the membrane fusion process (Berger et al., 1999;Gerard and Ro...

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Pyrimidine-specific regulation of the upstream carP1 promoter of the carbamoylphosphate synthase operon of Escherichia coli requires numerous trans-acting factors: the allosteric transcription regulator RutR, the nucleoid-associated protein integration host factor, and the trigger enzymes aminopeptidase A and PyrH (UMP-kinase). RutR, a TetR family member, binds far upstream of carP1. Here, we establish a high-resolution contact map of RutR•carP1 complexes for backbone and base-specific contacts, analyze DNA bending, determine the DNA sequence specificity of RutR binding by saturation mutagenesis, demonstrate that uracil but not thymine is the physiologically relevant ligand that inhibits the DNA binding capacity of RutR and build a model of the RutR·operator DNA complex based on the crystal structures of RutR and of the DNA-bound family member QacR. Finally, we test the validity of this model with site-directed mutagenesis of the helix–turn–helix DNA binding motif and in vitro binding studies with the cognate purified mutant RutR proteins.

Multifunctional Aminopeptidase A (PepA) from Escherichia coli is involved in the control of two distinct DNA transaction processes: transcriptional repression of the carAB operon, encoding carbamoyl phosphate synthase and site-specific resolution of ColE1-type plasmid multimers. Both processes require communication at a distance along a DNA molecule and PepA is the major structural component of the nucleoprotein complexes that underlie this communication. Atomic Force Microscopy was used to analyze the architecture of PepA·carAB and PepA·cer site complexes. Contour length measurements, bending angle analyses and volume determinations demonstrate that the carP1 operator is foreshortened by ∼235 bp through wrapping around one PepA hexamer. The highly deformed part of the operator extends from slightly upstream of the –35 hexamer of the carP1 promoter to just downstream of the IHF-binding site, and comprises the binding sites for the PurR and RutR transcriptional regulators. This extreme remodeling of the carP1 control region provides a straightforward explanation for the strict requirement of PepA in the establishment of pyrimidine and purine-specific repression of carAB transcription. We further provide a direct physical proof that PepA is able to synapse two cer sites in direct repeat in a large interwrapped nucleoprotein complex, likely comprising two PepA hexamers.