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Operator Regions, Genetic (0):
Recent article
Operator Regions, Genetic
Nucleic Acids Research (38)14 2010
Abstract
We describe a method for detecting protein-binding sites on chloroplast DNA, using modifications to the nuclear ChIP procedures. The method was developed using the lac operator (lacO)/lac repressor (LacI) system from Escherichia coli. The lacO sequences were integrated into a single site between the...
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PMID: 20484380
PDF is available here.
PDF is available here.
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Physical Review Letters (104)4 2010
Abstract
We show that minuscule entropic forces, on the order of 100 fN, can prevent the formation of DNA loops-a ubiquitous means of regulating the expression of genes. We observe a tenfold decrease in the rate of LacI-mediated DNA loop formation when a tension of 200 fN is applied to the substrate DNA, bia...
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PMID: 20366742
PDF is available here.
PDF is available here.
Abstract
We analyze the robust stability of this system which models the dynamics of both fast state, such as transcription and synthesis of free operator, and slow state, such as translation and tryptophan synthesis under consideration of nonlinear uncertainties. In addition, we analyze the role of these fe...
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PMID: 20865501
PDF is available here.
PDF is available here.
BMC Microbiology (10) 2010
Abstract
These results suggest multiple novel features for the regulation of these two adjacent operons. SiaR functions as both a repressor and an activator and SiaR and CRP interact to regulate both operons from a single set of operators....
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PMID: 20843349
PDF is available here.
PDF is available here.
Abstract
We have shown that binding helical residues have a very clear novel recognition sign. For 95.8% of total protein domains the binding polar residues of the recognizing alpha-helix were localized within one of the two largest clusters of polar side groups on the protein surface. In fact, we have seen...
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PMID: 19492865
PDF is available here.
PDF is available here.
Genetika (Moskva) (45)8 2009
Abstract
Plasmid pUC19-recAoc carrying a mutant allele of the recA gene, which plays the key role in the control of the SOS repair system and homologous recombinational repair, causes a 1.5-fold increase in radiation resistance of Escherichia coli DeltarecA cells, as compared to the wild-type recA+ cells. Th...
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PMID: 19769293
PDF is available here.
PDF is available here.
Abstract
We considered five of them and extended the observed regularities over the entire homeodomain family. The five complexes have been selected by similarity of protein structures and patterns of contacting residues. Their long range interactions and interfaces were compared. The long-range stage of the...
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PMID: 19385698
PDF is available here.
PDF is available here.
Nucleic Acids Research (37)8 2009
Abstract
We experimentally tested whether this relationship could be used to engineer novel DNA-protein interactions. Using Escherichia coli CRP as a template, we tested eight designs based on this relationship and found that four worked as predicted. Collectively, these results in this work demonstrate that...
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PMID: 19264798
PDF is available here.
PDF is available here.
Abstract
HPNikR is a prokaryotic nickel binding transcription factor found in the virulent bacterium Helicobacter pylori. HPNikR regulates the expression of multiple genes as an activator or repressor, including those involved in nickel ion homeostasis, acid adaptation, and iron uptake. The target operator s...
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PMID: 19119856
PDF is available here.
PDF is available here.
Abstract
We discuss the structure of LexA protein, particularly with respect to distinct conformations that enable repression of SOS genes via specific DNA binding or repressor cleavage during the response to DNA damage. These may provide new starting points in the battle against the emergence of bacterial p...
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PMID: 18726173
PDF is available here.
PDF is available here.
Molecular Microbiology (71)1 2009
Abstract
I footprint analysis was performed on the upstream regions of norB and nsrR, where NsrR was shown to protect the predicted 29 bp binding sites. The presence of exogenously added NO inhibited DNA binding by NsrR. Alanine substitution of C90, C97 or C103 in NsrR abrogated repression of norB::lacZ and...
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PMID: 19007408
PDF is available here.
PDF is available here.
Biophysical Journal (96)2 2009
Abstract
We investigated the binding interaction between the bacteriophage lambda-repressor CI and its target DNA using total internal reflection fluorescence microscopy. Large stepwise changes in the intensity of the red fluorescent protein fused to CI were observed as it associated with and dissociated fro...
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PMID: 19167308
PDF is available here.
PDF is available here.
Abstract
We calculated the mean rate of synthesis of the reporter protein and its standard deviation as a function of repressor concentration in cell. The theoretical relations fit well the experimental results. The results of calculations confirm the assumption that gene expression noise in a single cell at...
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PMID: 19795776
PDF is available here.
PDF is available here.
Journal of Molecular Biology (384)5 2008
Abstract
We present a 2.5-A structure of MtbArgR in complex with a 16-bp DNA operator in the absence of arginine. A biological trimer of the protein-DNA complex is formed via the crystallographic 3-fold symmetry axis. The N-terminal domain of MtbArgR has a winged helix-turn-helix motif that binds to the majo...
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PMID: 18952097
PDF is available here.
PDF is available here.
Journal of Molecular Biology (383)5 2008
Abstract
I footprinting assays indicated that Ni2+ is necessary and sufficient to promote HpNikR binding to PureA, while the effect of other metal ions in identical conditions is significantly lower (Zn2+ and Co2+) or absent (Ca2+ and Mg2+). Isothermal titration calorimetry (ITC) demonstrated the absence of...
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PMID: 18790698
PDF is available here.
PDF is available here.
Abstract
RepA, the replication initiator protein from the Pseudomonas plasmid pPS10, regulates plasmid replication and copy number. It is capable of autorepression, in which case it binds as a dimer to the inverted repeat operator sequence preceding its own gene. RepA initiates plasmid replication by binding...
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PMID: 18959764
PDF is available here.
PDF is available here.
Abstract
We investigated the molecular mechanism of how an Escherichia coli cell with the lac operon switches from one phenotype to another. At intermediate inducer concentrations, a population of genetically identical cells exhibits two phenotypes: induced cells with highly fluorescent membranes and uninduc...
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PMID: 18927393
PDF is available here.
PDF is available here.
Abstract
We directly examined in vitro loop formation mediated by Escherichia coli lactose repressor using single-molecule structural and kinetics methods. Small ( approximately 150 bp) loops form quickly and stably, even with out-of-phase operator spacings. Unexpectedly, repeated spontaneous transitions bet...
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PMID: 18828671
PDF is available here.
PDF is available here.
Environmental Microbiology (10)10 2008
Abstract
In bacteria, environmental challenges are often translated into a transcriptional response via the cognate response regulators (RRs) of specialized two-component systems (TCSs). A phylogenetic footprinting/shadowing approach was designed and used to identify many novel RR-specific operators for spec...
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PMID: 18662309
PDF is available here.
PDF is available here.
Journal of Molecular Biology (381)2 2008
Abstract
We tested the functional stability of replication forks reconstituted in vitro and blocked by lac repressor-operator complexes. Once a fork comes to a halt at such a block, it cannot continue subsequently to translocate through the block until addition of IPTG induces repressor dissociation. However...
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PMID: 18602646
PDF is available here.
PDF is available here.
Molecular Microbiology (69)4 2008
Abstract
We analyse mechanistic aspects of how RelE of Escherichia coli can function both as a co-repressor and as a derepressor of relBE transcription. When RelB was in excess to RelE, two trimeric RelB(2)*RelE complexes bound cooperatively to two adjacent operator sites in the relBE promoter region and rep...
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PMID: 18532983
PDF is available here.
PDF is available here.
Journal of Bacteriology (190)15 2008
Abstract
We investigated how these opposite effects are mediated by the same regulator. In vitro binding of purified PsaR to the prtA, pcpA, and psaB promoters was stimulated by Mn(2+), whereas Zn(2+) destroyed the interaction of PsaR with its target promoters. Mutational analysis of the pcpA promoter demons...
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PMID: 18515418
PDF is available here.
PDF is available here.
Microbial Pathogenesis (45)1 2008
Abstract
The Lyme disease spirochete Borrelia burgdorferi must repress expression of outer surface protein C (OspC) to effectively evade specific humoral immunity and to establish persistent infection. This ability largely relies upon a regulatory element, the only operator that has been reported in spirochet...
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PMID: 18479884
PDF is available here.
PDF is available here.
Journal of Bacteriology (190)13 2008
Abstract
We have undertaken mutagenesis experiments to convert ptsG from a gene regulated by Mlc into a gene regulated by NagC. There are two Mlc operators upstream of ptsG, and to switch ptsG to the NagC regulon, it was necessary to change two different characteristics of both operators. Firstly, we replace...
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PMID: 18469102
PDF is available here.
PDF is available here.
Journal of Molecular Biology (380)1 2008
Abstract
We present the NMR-derived structure of a RelB dimer and show that a RelB dimer recognizes a hexad repeat in the palindromic operator region through a ribbon-helix-helix motif. Our biochemical data show that two weakly associated RelB dimers bind to the adjacent repeats in the 3'-site of the operato...
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PMID: 18501926
PDF is available here.
PDF is available here.
Biotechnology Letters (30)6 2008
Abstract
We examine here new expression systems that have been described, including improvements of classical ones and new strategies of artificial gene control that have been applied in functional genomics....
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PMID: 18239858
PDF is available here.
PDF is available here.
FEMS Microbiology Letters (283)1 2008
Abstract
We propose that the SOS response indirectly regulates thermoregulation of colicin K (and possibly of the other examined colicins). Two LexA dimers bind cooperatively with high affinity to the two overlapping LexA boxes in a temperature-independent manner. At 22 degrees C the relative degree of repre...
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PMID: 18399998
PDF is available here.
PDF is available here.
Molecular Biotechnology (39)2 2008
Abstract
Although non-viral gene delivery is a very straightforward technology, there are currently no FDA-approved gene medicinal products available. Therefore, improving potency, safety, and efficiency of current plasmid DNA vectors will be a major task for the near future. This article will provide an ove...
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PMID: 18327557
PDF is available here.
PDF is available here.
Molecular Microbiology (68)3 2008
Abstract
We provide insight on a possible three-dimensional structure for two handcuffed arrays of the iterons found at the origin of pPS10 replicon. These are brought together in parallel register by zipping-up DNA-bound RepA monomers. We also present evidence for a distinct role of RepA dimers in DNA loopi...
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PMID: 18284592
PDF is available here.
PDF is available here.
Biophysical Journal (94)9 2008
Abstract
We show that these two modes of upregulation have very different effects on the promoter function. We predict that if CI(2) bound to O(R)2 produced equal increase in RNAP-DNA binding constant (compared to wild-type increase in the closed-open transition probability), the lysogen would be significant...
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PMID: 18400951
PDF is available here.
PDF is available here.
Biophysical Journal (94)9 2008
Abstract
We present a detailed analysis, based on the forward flux sampling simulation method, of the switching dynamics and stability of two models of genetic toggle switches, consisting of two mutually repressing genes encoding transcription factors (TFs); in one model (the exclusive switch), the two trans...
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PMID: 18222998
PDF is available here.
PDF is available here.
Journal of Bacteriology (190)9 2008
Abstract
We have shown previously that several N. gonorrhoeae Fur-repressed genes are expressed in vivo during mucosal gonococcal infection in men, which suggests that this organism infects in an iron-limited environment and that Fur is expressed under these conditions. In this study we have demonstrated exp...
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PMID: 18310343
PDF is available here.
PDF is available here.
Abstract
We used a fluorescent reporter protein to measure the CI concentration for a set of constructs that differ in their ability to assume various forms of the looped structure. Based on the observed steady-state fluorescence for these constructs, the presence of O(L) increases P(RM) activation unless bo...
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PMID: 18391225
PDF is available here.
PDF is available here.
FEBS Letters (582)7 2008
Abstract
We report the operator sites of the mce2R and its orthologs in other sequenced mycobacteria and non-mycobacterial species Nocardia farciana. All the identified DNA motifs illustrate the FadR subfamily specific nucleotide preference. Moreover, these motifs from the upstream region share sequence cons...
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PMID: 18329386
PDF is available here.
PDF is available here.
Molecular Microbiology (68)2 2008
Abstract
We investigated environmental regulation of two putative virulence determinants adcA and kfc by RegA, an AraC/XylS-like regulator, from Citrobacter rodentium, and identified bicarbonate as the environmental signal which induced transcription of adcA and kfc through RegA. Primer extension experiments...
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PMID: 18284589
PDF is available here.
PDF is available here.
Journal of Bacteriology (190)8 2008
Abstract
We experimentally identified that this system is transcribed from a single promoter with an initiation site located 110 nucleotides upstream of the ATG start codon. On the basis of computational data, it had been proposed that LldR and its homologue PdhR act as regulators of the lldPRD operon. Never...
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PMID: 18263722
PDF is available here.
PDF is available here.
Abstract
We describe a straightforward two-step PCR-based method to insert arrays of lac or tet operators (lacO or tetO) at specific loci in the budding yeast genome. The method entails insertion of a marker generated by PCR with classical long primers recognizing the locus of interest, followed by the repla...
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PMID: 18302313
PDF is available here.
PDF is available here.
Molecular Microbiology (67)4 2008
Abstract
We show that although CarA does bind vitamin B12, mutating the motif involved has no effect on its ability to repress P(B). Intriguingly, P(B) could be repressed in the dark even with no CarA, so long as B12 and an intact CarA operator were present. We have discovered that this effect of B12 depends...
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PMID: 18315685
PDF is available here.
PDF is available here.
Journal of Bacteriology (190)4 2008
Abstract
We describe 37 genes regulated in a LexA-dependent manner in the alphaproteobacterium Caulobacter crescentus. In agreement with previous results, we have found that the direct repeat GTTCN7GTTC is the SOS operator of C. crescentus, which was confirmed by site-directed mutagenesis studies of the imuA...
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PMID: 18083815
PDF is available here.
PDF is available here.
BMC Genomics (9)1 2008
Abstract
When the approach was applied to the 12 LacI-family TFs of the model species, a specific operator motif was identified for each of them. With the TF-specific operator motifs, potential binding sites were found on the genome and putative minimal regulons could be defined. Moreover, specific inducers...
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PMID: 18371204
PDF is available here.
PDF is available here.
Molecular Microbiology (67)2 2008
Abstract
We have isolated mutations in both proteins which prevent the inactivation of the repressors by growth on glucose or GlcNAc. These mutations are located in different and specific regions of each protein. For Mlc changes at the C-terminal make it a constitutive repressor and also prevent it from bind...
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PMID: 18067539
PDF is available here.
PDF is available here.
Abstract
We created a new DNA recognition specificity for tetracycline repressor (TetR) binding to the tet operator variant tetO-4C5G containing four bp exchanges compared to tetO. TetR variants created by doped oligonucleotide mutagenesis of residues in the DNA recognition helix yielded several mutants bind...
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PMID: 17928170
PDF is available here.
PDF is available here.
Molecular Microbiology (66)6 2007
Abstract
We report that a fis mutant of E. chrysanthemi showed a strong increase in transcription of the pel genes during exponential growth whereas induction of expression in the parental strain occurred at the end of exponential growth. This reveals that Fis acts to prevent an efficient transcription of pe...
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PMID: 18028312
PDF is available here.
PDF is available here.
Journal of Bacteriology (189)24 2007
Abstract
We show here that P(xylX) and at least one other promoter in the xylose regulon (P(xylE)) are controlled by the CC3065 (xylR) gene product, a LacI-type repressor. Electrophoretic gel mobility shift assays showed that operator binding by XylR is greatly reduced in the presence of D-xylose. The data s...
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PMID: 17933895
PDF is available here.
PDF is available here.
Current protocols in protein science / editorial board, John E. Coligan ... [et al.] (Chapter 5) 2007
Abstract
Despite the development of various nonbacterial expression systems, Escherichia coli (E. coli) remains the host of choice for recombinant protein expression. Its culture is simple, fast, inexpensive, and highly efficient (tens of milligrams of pure proteins are typically obtained within 48 hours usi...
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PMID: 18429327
PDF is available here.
PDF is available here.
FEBS Letters (581)25 2007
Abstract
We performed molecular dynamic simulations of two LexA dimers bound to operators. Our model predicted that rotation of the LexA DNA binding domain, with respect to the dimerised C-terminal domain, is required for selective DNA binding. To confirm the model, double and quadruple cysteine LexA mutants...
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PMID: 17884043
PDF is available here.
PDF is available here.
Abstract
To gain insight into the structure and function of repressor proteins of bacteriophages of gram-positive bacteria, repressor of temperate Staphylococcus aureus phage phi11 was undertaken as a model system here and purified as an N-terminal histidine-tagged variant (His-CI) by affinity chromatography...
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PMID: 17927908
PDF is available here.
PDF is available here.
Abstract
We found that the binding of rhodamine 6G to AcrR is inhibited by the presence of ethidium. In contrast, the dissociation constant of proflavin binding to AcrR was not affected by ethidium, a result suggesting that ethidium and proflavin are bound to distinct binding sites....
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PMID: 17644067
PDF is available here.
PDF is available here.
Journal of Bacteriology (189)18 2007
Abstract
We have developed Escherichia coli-based biosensors that accurately report the regulatory activity of these proteins and used it to investigate their interactions with DNA and small-molecule ligands. We found that the SCO7222 protein and ActR repress the expression of their putative target genes, SC...
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PMID: 17644591
PDF is available here.
PDF is available here.
Abstract
We formulate a model of lac induction taking due account of the tetrameric structure of the repressor and the existence of looped complexes. We show that: (1) The kinetics are significantly more cooperative than those predicted by the Yagil and Yagil model. The cooperativity is higher because the fo...
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PMID: 17490688
PDF is available here.
PDF is available here.
Abstract
The lysogeny region of the Lactobacillus delbrueckii bacteriophage mv4 contains two divergently oriented ORFs coding for the Rep (221 aa) and Tec (64 aa) proteins. The transcription of these two genes was analysed by primer extension and Northern blot experiments on lysogenic strains. The location o...
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PMID: 17412387
PDF is available here.
PDF is available here.
Journal of Molecular Biology (369)5 2007
Abstract
We propose a model for the binding of TtgR to its target sequence....
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PMID: 17498746
PDF is available here.
PDF is available here.
Abstract
We present evidence, albeit indirect, that the RpoS effect occurs via psyR. Thus, AefR positively regulates AHL production, whereas RpoS has a strong negative effect. We show that AefR and RpoS do not regulate PsrA and that the PsrA effect on AHL production is exerted via its cumulative, but indepen...
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PMID: 17400767
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (282)22 2007
Abstract
We determined the binding parameters of the most efficient effectors for TtgV and its mutant variants. All mutants bound biaromatic compounds with higher affinity than the wild-type protein, whereas monoaromatic compounds were bound with lower affinity. This tendency was particularly pronounced for...
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PMID: 17416591
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (282)22 2007
Abstract
We screened a chemical library of more than 150 metabolic scaffolds using a high-throughput protein stability assay to identify molecules that bind IclR and then tested the active compounds in in vitro assays of operator binding. Glyoxylate and pyruvate, identified by this method, bound the C-IclR d...
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PMID: 17426033
PDF is available here.
PDF is available here.
Abstract
We directly observed specific binding of a lac repressor, labeled with a fluorescent protein, to a chromosomal lac operator. Using single-molecule detection techniques, we measured the kinetics of binding and dissociation of the repressor in response to metabolic signals. Furthermore, we characteriz...
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PMID: 17525339
PDF is available here.
PDF is available here.
Biophysical Journal (92)9 2007
Abstract
We present here analytical ultracentrifugation and fluorescence anisotropy experiments that demonstrate that CggR binds as a tetramer to the full-length operator DNA in a highly cooperative manner. We also show that CggR binds as a dimer to each direct repeat, the affinity being approximately 100-fo...
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PMID: 17293407
PDF is available here.
PDF is available here.
Molecular Microbiology (64)1 2007
Abstract
We show that a large palindromic sequence immediately upstream of the ospC promoter is essential for the repression of ospC expression during murine infection and for the ability of B. burgdorferi to evade specific OspC humoral immunity. Deletion of the sequence completely diminished the ability of...
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PMID: 17376084
PDF is available here.
PDF is available here.
Molecular Microbiology (64)1 2007
Abstract
We sequenced the immunity regions of several wild phages with the immunity specificity of lambda, both to determine whether natural variation exists in regulation, and to analyse conservation and variability in a region rich in well-studied regulatory elements. CI, Cro and their cis-acting sites are...
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PMID: 17376085
PDF is available here.
PDF is available here.
Biophysical Chemistry (126)1-3 2007
Abstract
We examine sugars that bind the lactose repressor protein (LacI) and modify repressor affinity for operator DNA using isothermal titration calorimetry and equilibrium DNA binding experiments. High affinity binding of the commonly-used inducer isopropyl-beta,D-thiogalactoside is strongly driven by en...
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PMID: 16860458
PDF is available here.
PDF is available here.