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DNA Binding Sites (dna + binding_site)
Selected AbstractsThe iron dependent regulatory protein IdeR (DtxR) of Rhodococcus equiFEMS MICROBIOLOGY LETTERS, Issue 1 2000Clara A. Boland Abstract This paper reports the presence of an ideR gene, which encodes an iron-dependent regulatory protein, in Rhodococcus erythropolis and in the intracellular pathogen Rhodococcus equi. The ideR gene of the latter encoded a protein of 230 amino acids with a molecular mass of 25,619. The ,-helices forming the helix-turn-helix motif of the R. equi protein were identical to those of the DtxR protein of Corynebacterium diphtheriae, which is an IdeR homologue. This indicates that the two proteins bind to the same DNA binding site. This was confirmed following expression of IdeR in Escherichia coli, which showed that the IdeR protein could repress transcription of the tox promoter of C. diphtheriae in an iron dependent manner. An open reading frame specifying a 283-amino acid polypeptide similar to galE encoding UDP-galactose 4-epimerase was present downstream of the ideR gene. [source] Significance of consensus CYC-binding sites found in the promoters of both ChCYC and ChRAD genes in Chirita heterotricha (Gesneriaceae)JOURNAL OF SYSTEMATICS EVOLUTION, Issue 4 2010Xia YANG Abstract,CYC -like genes are widely conserved in controlling floral dorsoventral asymmetry (zygomorphy) through persistent expression in corresponding domains in core eudicots. To understand how CYC -like gene expression is maintained during flower development, we selected Chirita heterotricha as a material and isolated the promoter sequences of the ChCYC1C and ChCYC1D genes, homologs of CYC, by inverse polymerase chain reaction. Further promoter analyses led to the identification of a putative cis -regulatory element in each promoter matching the consensus DNA binding site for Antirrhinum CYC protein: GGCCCCTC at ,165 for ChCYC1C, and GGCCCCCC at ,163 for ChCYC1D. This indicates that both the ChCYC1C and ChCYC1D genes have probably evolved autoregulatory loops to sustain their expression in developing flowers. We also isolated the coding and promoter sequences of the ChRAD gene, a homolog of Antirrhinum RAD. Promoter analysis showed that the ChRAD gene promoter also contained a putative CYC-binding site (GGCCCAC at ,134). Therefore, ChRAD is likely a direct target of the ChCYC1 genes, which is similar to Antirrhinum RAD. These results imply that the establishment of floral zygomorphy in Chirita may have been achieved by the evolution of an autoregulatory loop for CYC -like genes, which was probably accompanied by simultaneous co-option of the RAD -like gene into their regulatory network. [source] Real-time observation of Wnt ,-catenin signaling in the chick embryoDEVELOPMENTAL DYNAMICS, Issue 1 2010Anne C. Rios Abstract A critical mediator of cell,cell signaling events during embryogenesis is the highly conserved Wnt family of secreted proteins. Reporter constructs containing multimerized TCF DNA binding sites have been used to detect Wnt ,-catenin dependent activity during animal development. In this report, we have constructed and compared several TCF green fluorescent protein (GFP) reporter constructs. They contained 3, 8, or 12 TCF binding sites upstream of a minimal promoter driving native or destabilized enhanced GFP (EGFP). We have used the electroporation of somites in the chick embryo as a paradigm to test them in vivo. We have verified that they all respond to Wnt signaling in vivo. We have then assessed their efficiency at reflecting the activity of the Wnt pathway. Using destabilized EGFP reporter constructs, we show that somite cells dynamically regulate Wnt/,-catenin,dependent signaling, a finding that was confirmed by performing time-lapse video confocal observation of electroporated embryos. Developmental Dynamics 239:346,353, 2010. © 2009 Wiley-Liss, Inc. [source] Members of the IclR family of bacterial transcriptional regulators function as activators and/or repressorsFEMS MICROBIOLOGY REVIEWS, Issue 2 2006Antonio J. Molina-Henares 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. [source] MicroReview: LuxR-type quorum-sensing regulators that are detached from common scentsMOLECULAR MICROBIOLOGY, Issue 5 2010Ching-Sung Tsai Summary The ability of LuxR-type proteins to regulate transcription is controlled by bacterial pheromones, N-acylhomoserine lactones (AHLs). Most LuxR-family proteins require their cognate AHLs for activity, and at least some of them require AHLs for folding and protease resistance. However, a few members of this family are able to fold, dimerize, bind DNA, and regulate transcription in the absence of AHLs; moreover, these proteins are antagonized by their cognate AHLs. Complexes between some of these proteins and their DNA binding sites are disrupted by AHLs in vitro. All such proteins are fairly closely related within the larger LuxR family, indicating that they share a relatively recent common ancestor. The 3, ends of the genes encoding these receptors invariably overlap with the 3, ends of the cognate AHL synthase genes, suggesting additional antagonism at the level of mRNA synthesis, stability or translation. [source] Control of nitrogen metabolism by Bacillus subtilis glutamine synthetaseMOLECULAR MICROBIOLOGY, Issue 2 2008Abraham L. Sonenshein Summary Two recent papers describe the molecular mechanism by which the activity of GlnR, the repressor of the glutamine synthetase operon in Bacillus subtilis, is stimulated by glutamine-bound (i.e. feedback-inhibited) glutamine synthetase (FBI-GS). Remarkably, FBI-GS acts as a molecular chaperone to stabilize the association of GlnR dimers with their DNA binding sites. This mechanism allows the cell to shut off synthesis of GS, and hence of glutamine, when both the enzyme and its product are in excess. FBI-GS also regulates the activity of TnrA, the global regulator of nitrogen metabolism genes, but by a very different mechanism. Thus, the same enzyme,metabolite complex has two different roles in transcriptional regulation. [source] | ||||||||||