Assays for transcription factor activity.
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Binding Sites↗
Biomedical subjects
A Kolb
Publications and source records attributed to A Kolb.
E. coli RNA polymerase, deleted in the C-terminal part of its alpha-subunit, interacts differently with the cAMP-CRP complex at the lacP1 and at the galP1 promoter.
A deletion of the C-terminal part of the alpha-subunit of RNA polymerase is known to affect differently promoters activated by CRP depending on the location of the CRP binding site at the promoter. When the CRP binding site is located at -61.5, as at lacP1 (a type I promoter), activation is strongly impaired while it is not significantly affected at galP1 where CRP binds 41.5 bp upstream of the start of the message (type II promoter). We have investigated the differences in the architecture of the corresponding open complexes by comparing the positioning of holoenzymes reconstituted respectively with native or with truncated alpha-subunits (containing the first 235 or 256 residues of a) at two 'up' promoter mutants of the lacP1 and galP1 promoters (respectively lacUV5 and gal9A16C). First, the affinity of wild-type RNA polymerase for both promoters is increased by the presence of CRP and cAMP. By contrast, holoenzymes reconstituted with truncated alpha-subunits, show cooperative binding at the galP1 promoter only. Second, footprinting data confirm these observations and indicate that the truncated holoenzymes are unable to recognize regions of the promoter upstream from position -40. The absence of contacts between the truncated enzymes and CRP at the lacP1 promoter can explain the deficiency in activation. At the galP1 promoter, where the CRP site is closer to the initiation site, protein-protein contacts can still occur with the truncated polymerases, showing that the C-terminal part of the alpha-subunit is not involved in activation.
Carrier Proteins↗
DNA loop formation between Nag repressor molecules bound to its two operator sites is necessary for repression of the nag regulon of Escherichia coli in vivo.
Binding sites for the Nag repressor overlap the transcription start sites of the divergent nagE and nagB genes, such that the centres of the sites are separated by nine turns of the B-DNA helix. Mutations which prevent repressor binding to either site or alter the phasing of the binding sites result in simultaneous derepression of both genes. An additional mutation which restores the phasing of the two sites permits repression. These observations show that repression is the result of co-operative binding of the repressor to its two sites, resulting in the formation of a loop of DNA.
Bacterial Proteins↗
Transcriptional regulation by cAMP and its receptor protein.
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Allosteric Regulation↗
Transcription activation by cAMP receptor protein (CRP) at the Escherichia coli gal P1 promoter. Crucial role for the spacing between the CRP binding site and the -10 region.
The cAMP-CRP complex activates the initiation of transcription at the Escherichia coli gal P1 promoter, and the activation efficiency is highly sensitive to the location of the complex on this promoter region. Moving the CRP binding site by one base pair toward the start of transcription significantly decreases the extent of activation in vivo and actually turns the cAMP-CRP complex into an inhibitor in in vitro experiments. A structural analysis of open complexes formed on the two promoter fragments at 37 degrees C has revealed three elements crucial for an optimal activation process: a strong upstream anchorage of RNA polymerase, a cooperative binding of CRP and RNA polymerase, and an accurate orientation of the two promoter regions located upstream and downstream of the CRP binding site. Furthermore, structural analysis of polymerase promoter complexes at lower temperatures suggests that RNA polymerase initially recognizes the upstream region of the gal P1 promoter and subsequently interacts with sequences from the -10 to +20 region to yield the final open complex structure. The involvement of CRP in these sequential events has been examined.
Base Sequence↗
Positive regulation of the expression of the Escherichia coli pts operon. Identification of the regulatory regions.
The pts operon of Escherichia coli is composed of the ptsH, ptsI and crr genes coding for three proteins central to the phosphoenolpyruvate dependent phosphotransferase system (PTS), the HPr, enzyme I and EIIIGlc proteins, respectively. We previously showed that transcription from the promoter region located upstream from the pts operon is regulated by two control circuits, which can occur independently from each other. Transcription of the pts operon is (1) stimulated by the CAP-cAMP complex and (2) enhanced during growth on glucose, a PTS substrate. The DNA regions involved in regulation of the expression of the pts operon have been identified. Two promoters, P0 and P1, separated by 100 bp are located upstream from the pts operon. In these promoter regions, we identified two sequences showing similarity with the consensus of CAP-binding sites, CAPa located near P0 and CAPb located in the -35 region of P1. In vivo experiments showed that binding of CAP-cAMP at the CAPa site stimulates transcription from the P0 promoter. The binding sites of CAP-cAMP and/or RNA-polymerase on a DNA fragment containing both P0 and P1 promoters as well as both CAPa and CAPb sites were examined by the technique of DNase I footprinting. These in vitro experiments suggested that CAP-cAMP binding at the CAPb site might also play a role in regulation of the pts operon expression. In addition, we showed that the DNA region carrying the CAPa site is important for regulation by glucose. We finally propose that the expression of the pts operon is controlled by two alternative positive regulatory mechanisms, which are designed to allow activation of the pts operon under a great variety of growth conditions.
Amino Acid Sequence↗
Upstream curved sequences influence the initiation of transcription at the Escherichia coli galactose operon.
The two overlapping promoters that control mRNA synthesis at the galactose operon contain three phased stretches of adenine residues, located around positions -84.5, -74 and -63, with respect ot the start of the P1 promoter. As a result, the corresponding DNA sequence is bent, an anomaly that is relieved by the addition of small concentrations of drugs like distamycin A or netropsin. By abortive initiation assays performed on several DNA fragments derived from the wild-type promoter or from various mutants we show that the curved sequence increases the strength of the P1 promoter. In the absence of cyclic AMP (cAMP) and of the corresponding receptor protein (CRP), the upstream curved sequences enhance the rate of isomerization from the closed to the open complex at P1. This effect is abolished when distamycin A is bound in the bent region. In the presence of cAMP-CRP, a more drastic change is observed: activation of the gal P1 promoter takes place at a different formal step, depending whether the upstream curved sequence is present or not (enhancement of the rate of conversion from a closed to an open complex instead of an increase in the affinity of the enzyme during closed complex formation). These data, together with previous results obtained with other mutants of the gal control region, suggest that several closed complexes corresponding to different nucleoprotein arrangements are formed during open complex formation at gal P1, in the presence of CRP.
Base Sequence↗
Protein-DNA cross-linking at the lac promoter.
We report the results of photo-cross-linking of RNA polymerase and the cyclic AMP receptor protein (CRP) to the lac UV5 promoter region carried on either a linear fragment or a supercoiled plasmid. We have devised a protocol that allows the localisation of bases in contact with the protein. RNA polymerase makes contacts within the -10 and -35 regions of the promoter, essentially on the non-template strand. The CRP contact points found in a binary complex are affected by the formation of the ternary complex containing RNA polymerase. Supercoiling has no effect on the position of contacts in any of the complexes. These conclusions were derived from experiments performed using a generally applicable, non-interfering technique that reveals direct contacts between proteins and nucleic acids in nucleoprotein complexes.
Base Sequence↗
CAP and Nag repressor binding to the regulatory regions of the nagE-B and manX genes of Escherichia coli.
The divergent nagE-BACD operons located at 15.5 min on the Escherichia coli chromosome encode genes involved in the uptake and metabolism of N-acetylglucosamine. The start sites of the divergent transcripts are separated by 133 base-pairs (bp). A repressor protein for the regulon is encoded by the gene nagC, one of the genes of the nagBACD operon. Strains overproducing the NagC protein have been used to investigate the binding of repressor to the intergenic nagE-B regulatory region. Two binding sites have been detected, overlapping the promoters of the nagE and nagB genes. NagC binding produces a series of DNase I hypersensitive sites separated by 9 to 11 bp in the region between the two NagC binding sites, supporting a model where the NagC proteins bind co-operatively to these two sites on the DNA and interact to form a DNA loop. A strong CAP binding site exists between the two operator sites. It is located at -61.5 and -71.5 relative to the nagE and nagB transcription start sites. CAP and NagC can bind simultaneously and produce a complex more stable than the binary NagC-DNA complex. In addition NagC and CAP binding sites have been found upstream from the manXYZ operon. Although the sites exhibit a similar organization there is no evidence for formation of a DNA loop in this operon.
Acetylglucosamine↗
Lithotripsy of gallstones by means of a quality-switched giant-pulse neodymium:yttrium-aluminum-garnet laser. Basic in vitro studies using a highly flexible fiber system.
The quality-switched neodymium:yttrium-aluminum-garnet laser represents a new instrument for athermal fragmentation of gallstones by transformation of optical energy into mechanical energy in the form of shock waves via local plasma formation. A highly flexible 300-micron fiber transmission system was used in basic investigations to determine the influence of varying pulse repetition rates (5-30 Hz) and pulse energies (15 and 20 mJ) on shock wave intensity and stone fragmentation in vitro for 105 biliary calculi of known size and chemical composition. After performance of 1200 shock wave pressure measurements using polyvinylidenefluoride hydrophones, stone fragmentation was analyzed by determination of fragment removal rates (volume of fragments removed per fragmentation time), ablation rates (mean volume removed per laser pulse), and median fragment sizes for each laser setting. With the quality-switched neodymium:yttrium-aluminum-garnet laser system, all concrements could be reliably disintegrated into small fragments (median diameter, 0.7-1.7 mm). Compared with pure cholesterol stones, a significantly higher fragment removal rate was achieved in cholesterol stones containing 30% calcium phosphate (P = 0.039), in cholesterol stones containing 20% pigment (P = 0.015), and in pure pigment stones (P = 0.007). Fragment removal rates, local shock wave pressures, and median grain sizes were significantly higher at a pulse energy of 20 mJ than with 15 mJ. Shock wave pressures showed a distinct dependence on pulse repetition rates at 20 mJ, yet not at 15 mJ. Because there is no evident hazard of thermal damage to tissue using the quality-switched neodymium:yttrium-aluminum-garnet laser, it appears to be a promising device for nonsurgical biliary stone therapy.
Aluminum↗
Mutations that alter the ability of the Escherichia coli cyclic AMP receptor protein to activate transcription.
The effects of a number of mutations in the E. coli cyclic AMP receptor protein (CRP) have been determined by monitoring the in vivo expression and in vitro open complex formation at two semi-synthetic promoters that are totally CRP-dependent. At one promoter the CRP-binding site is centered around 41.5 base pairs upstream from the transcription start whilst at the other promoter it is 61.5 base pairs upstream. The CRP mutation E171K reduces expression from both promoters whilst H159L renders CRP totally inactive: neither mutation stops CRP binding at either promoter. The mutations K52N and K52Q reverse the effect of H159L and 'reeducate' CRP to activate transcription. CRP carrying both H159L and K52N activates transcription from the promoter with the CRP site at -41.5 better than wild type CRP. In sharp contrast, this doubly changed CRP is totally inactive with respect to the activation of transcription from the promoter carrying the CRP site at -61.5. Our results suggest that CRP can use different contacts and/or conformations during transcription activation at promoters with different architectures.
Amino Acid Sequence↗
Stringent spacing requirements for transcription activation by CRP.
The cyclic AMP receptor protein-cAMP complex (CRP-cAMP) binds at a variety of distances upstream of several E. coli promoters and activates transcription. We have constructed a model system in which a consensus CRP binding site is placed at different distances upstream of the melR promoter. CRP-cAMP activates transcription from melR when bound at a number of positions, all of which lie on the same face of the DNA helix. The two distances at which transcription is strongly activated correspond exactly to those at which CRP-cAMP binds upstream of the well-studied galP1 and lac promoters. Footprinting of the synthetic promoters reveals that RNA polymerase makes identical contacts with their -10 regions even though CRP-cAMP binds at a different distance in each case. Kinetic analysis in vitro indicates that CRP-cAMP activates transcription from these promoters in similar but distinct ways. A model is proposed to explain this two-position activation.
Base Sequence↗
Synthetic curved DNA sequences can act as transcriptional activators in Escherichia coli.
Can a transcriptional activator known to bend DNA be functionally replaced by a sequence-directed bend in Escherichia coli? To investigate this question, a partially truncated promoter was used, deleted of its -35 region and of its CRP binding site, leaving only two Pribnow boxes as functional elements. Synthetic and naturally occurring curved DNA sequences introduced upstream from these elements could restore transcription at either one of the two natural starts. Some of these hybrid promoters turned out to be more efficient than the CRP activated wild-type gal promoter in vivo. Control experiments performed with very similar sequences devoid of any curvature produced weak promoters only. Minimal changes in the location of the centre of curvature or perturbation in the amount of curvature strongly affected the level of expression. No significant stimulation of transcription could be detected in vitro. Furthermore, both gal P1 and P2 starts could be activated in vivo but also in vitro via a properly positioned CRP binding site. This partial analogy suggests that bending induced by the cAMP-CRP complex upon binding to its site may be biologically relevant to the mechanism of transcriptional activation.
Base Sequence↗
Binding of the Escherichia coli cyclic AMP receptor protein to DNA fragments containing consensus nucleotide sequences.
Binding of the Escherichia coli CRP protein to DNA fragments carrying nucleotide sequences closely corresponding to the consensus is very tight with a dissociation time of over 2 h in our conditions. The concentration of cyclic AMP required for this binding is below the physiological range of intracellular cyclic AMP concentrations. Changes in nucleotide sequence at positions that are not well-conserved between different naturally-occurring CRP sites allow a more rapid dissociation of CRP-DNA complexes. There is an inverse correlation between the stability of CRP binding to sites in vitro and the repression by glucose of expression dependent on these sites in vivo: expression that is dependent on the tighter binding sites cannot be repressed by the inclusion of glucose in the growth medium.
Base Sequence↗
Protein-induced unwinding of DNA: measurement by gel electrophoresis of complexes with DNA minicircles. Application to restriction endonuclease EcoRI, catabolite gene activator protein and lac repressor.
An electrophoretic procedure for the measurement of the helix unwinding induced by a sequence-specific protein is described. The method, which was applied here to EcoR I, CAP and lac repressor, involved the migration of the complexes with positively and negatively supercoiled DNA minicircles carrying a single protein binding site. Mobility shifts of complexes relative to naked DNAs appeared to be a result of i) the unwinding; of ii) an increase in the molecular frictional coefficient, which led to a retardation; of iii) bending, in the particular case of CAP, which induced an acceleration; and of iv) looping, in the case of lac repressor, which also resulted in an acceleration. Under conditions where the migration of the naked topoisomers was V-like (topoisomer mobility showed the same linear increase with both negative and positive supercoilings; Zivanovic et al. (1986) J. Mol. Biol., 192, 645-660), the protein unwinding contribution to mobility was assumed to be identical to that experimentally observed in the case of a thermal unwinding: all negatively supercoiled topoisomers were retarded and all positively supercoiled topoisomers were accelerated to the same extent. In contrast, the mobility contribution of the frictional term, as well as those of bending and looping, appeared to vary strongly with the magnitude of the supercoiling, but only weakly with its polarity. As a consequence, these latter contributions may approximately cancel when one is measuring the difference between the shifts observed for two comigrating, negatively and positively supercoiled, topoisomers, allowing the unwinding to be calculated. While estimates obtained for EcoR I, 23 +/- 3 degrees, and CAP, about 29 degrees, were in good agreement with previous measurements using topoisomerase I, the value found for lac repressor, 13 to 16 degrees, was significantly smaller.
Base Composition↗
Alterations in the binding site of the cyclic AMP receptor protein at the Escherichia coli galactose operon regulatory region.
Gene manipulation techniques have been used to alter the binding site for the cyclic AMP-cyclic AMP receptor protein complex (cAMP-CRP) at the regulatory region of the Escherichia coli galactose (gal) operon. The effects of these changes on CRP-dependent stimulation of expression from the galP1 promoter in vivo have been measured, and gel binding assays have been used to measure the affinity of cAMP-CRP for the modified sites. Firstly we have deleted progressively longer sequences from upstream of the gal CRP site in order to locate the functional limit of the site. A deletion to -49, removing the first base that corresponds to the consensus sequence for a CRP binding site, is sufficient to reduce CRP binding and block CRP-dependent stimulation of P1. Secondly, we used synthetic oligonucleotides to invert the asymmetric nucleotide sequence at the gal CRP binding site or to make the sequence symmetric. Inversion of the site has little effect on CRP binding, the architecture of open complexes at P1 revealed by DNAase I footprinting, or the stimulation of transcription from P1. Making the site symmetric increases the affinity for CRP by over 50-fold and leads to increased transcription from P1, whilst hardly altering the DNAase I footprint of open complexes. Our results confirm that the strength of binding of CRP depends on the nature of the site and show that it is this that principally accounts for differences in CRP-dependent stimulation of transcription.
Base Sequence↗
A new target for CRP action at the malT promoter.
In Escherichia coli, the transcription of the malT gene is activated by the complex formed between cAMP and its receptor protein, CRP. Kinetics of formation of polyribonucleotide products from the corresponding promoter were studied in vitro by two sets of techniques, abortive initiation assays and run-off experiments. The first type of assay indicated that open complexes were formed at malT with an equivalent efficiency, and at comparable rates, whether CRP-cAMP was present or not. Secondary effects due to the activating complex were observed (increased stability of the open complex, elimination of a weaker binding site for the enzyme, improved Michaelis constants of RNA polymerase for the substrates of the assay, UTP in particular). But, primarily, CRP-cAMP did not exert a significant role in the rate of formation of the initiation complex. In contrast, run-off assays showed that the yield of the full-length transcripts was markedly enhanced by prior incubation of the DNA fragment with CRP-cAMP. Both in the presence and in the absence of activator, the rate-limiting step for this process was markedly slower than the formation of the initial open complex. Short oligonucleotides (n less than 9), probably arising from a recycling process, were found when the initiation complex was formed in the absence of CRP-cAMP. They were abolished by prior incubation with the activator. Unexpectedly, CRP-cAMP appears to favour the escape of RNA polymerase from the initiation complex at this promoter.
Base Sequence↗
[Monozygotic twins suffered the same disease within 24 hours].
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Diseases in Twins↗