Members of the IclR family of bacterial transcriptional regulators function as activators and/or repressors

Abstract

Members of the IclR family of regulators are proteins with around 250 residues. The IclR family is best defined by a profile covering the effector binding domain. This is supported by structural data and by a number of mutants showing that effector specificity lies within a pocket in the C-terminal domain. These regulators have a helix-turn-helix DNA binding motif in the N-terminal domain and bind target promoters as dimers or as a dimer of dimers. This family comprises regulators acting as repressors, activators and proteins with a dual role. Members of the IclR family control genes whose products are involved in the glyoxylate shunt in Enterobacteriaceae, multidrug resistance, degradation of aromatics, inactivation of quorum-sensing signals, determinants of plant pathogenicity and sporulation. No clear consensus exists on the architecture of DNA binding sites for IclR activators: the MhpR binding site is formed by a 15-bp palindrome, but the binding sites of PcaU and PobR are three perfect 10-bp sequence repetitions forming an inverted and a direct repeat. IclR-type positive regulators bind their promoter DNA in the absence of effector. The mechanism of repression differs among IclR-type regulators. In most of them the binding sites of RNA polymerase and the repressor overlap, so that the repressor occludes RNA polymerase binding. In other cases the repressor binding site is distal to the RNA polymerase, so that the repressor destabilizes the open complex.

Bacterial quorum sensing and metabolic slowing in a cooperative population

“…Repression of multiple genes by QsmR is not unusual because IclRtype transcriptional regulators have been shown to function as both activators and repressors in other bacteria (26). Repression of multiple enzymes involved in glucose uptake and primary metabolism by QsmR is therefore a normal aspect of QS, but also the result of indirect control of QS in B. glumae.…”

“…In AHL QS-mediated gene regulation, a LuxR-type regulator can act as either a transcriptional activator or a repressor (26)(27)(28) although evidence of simultaneous activation and repression is relatively rare. According to genome-wide AHL-dependent analyses of Pseudomonas aeruginosa and other bacteria, there are indications that QS negatively influences gene expression (29,30).…”

Laboratory evolution of Geobacter sulfurreducens for enhanced growth on lactate via a single-base-pair substitution in a transcriptional regulator

“…The specific function of a novel IclR family protein cannot be predicted simply by sequence similarity Molina-Henares et al, 2006). One potential difference in growth on lactate versus growth on acetate (Figure 4a) is the necessity for succinyl-CoA synthase for growth on lactate (Figure 4b).…”

Functional Identification of OphR, an IclR Family Transcriptional Regulator Involved in the Regulation of the Phthalate Catabolic Operon in Rhodococcus sp. Strain DK17

“…4b). It is generally known that the respective binding sites of RNA polymerase and the repressor overlap in most IclR-type regulators so that the repressor blocks the RNA polymerase binding [13,14]. Combined with that fact, the dissociation of the OphR-IR complex by phthalate suggests that OphR acts as a repressor of the expression of the phthalate operon by occupying the regulatory region.…”