Gene/Protein Disease Symptom Drug Enzyme Compound
Pivot Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound   Target Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound

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Query: EC:2.7.7.6 (RNA polymerase)
34,946 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

A variety of reports describe shifts in the environment which cause a corresponding change in the measured linking number of plasmid DNA isolated from bacterial cells. This change in linking number is often attributed to a change in superhelical density. This, coupled with the observation that transcription is often dependent upon the superhelical density of the DNA template seen in vitro, has led to the suggestion that superhelical density may control expression of certain genes. However, since many environmental changes could, in principle, influence DNA twist itself, then the measured differences in linking number, delta Lk, may simply be a consequence of variation in twist according to the relationship delta Lk = delta Tw + delta Wr, where delta Tw and delta Wr are changes in twist and writhe, respectively. In fact, we show that when an environmental change causes a change in the helical pitch of the DNA, and if the superhelical density of DNA is regulated to remain constant according to the homeostatic model of Menzel and Gellert, then delta Lk approximately delta Tw. We have found that there are a number of published reports describing variation in promoter activity as a function of linking number that can be explained by considering twist. We suggest that there are classes of sigma 70 promoters whose ability to be recognized by RNA polymerase is exquisitely sensitive to the relative orientation of the -35 and -10 regions, and environmental conditions can control this relative orientation by changing DNA twist.(ABSTRACT TRUNCATED AT 250 WORDS)
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PMID:DNA twist as a transcriptional sensor for environmental changes. 150 37

Positive control of transcription often involves stimulatory protein-protein interactions between regulatory factors and RNA polymerase. Critical steps in the activation process itself are seldom ascribed to protein-DNA distortions. Activator-induced DNA bending is typically assigned a role in binding-site recognition, alterations in DNA loop structures or optimal positioning of the activator for interaction with polymerase. Here we present a transcriptional activation mechanism that does not require a signal-induced DNA bend but rather a receptor-induced untwisting of duplex DNA. The allosterically modulated transcription factor MerR is a repressor and an Hg(II)-responsive activator of bacterial mercury-resistance genes. Escherichia coli RNA polymerase binds to the MerR-promoter complex but cannot proceed to a transcriptionally active open complex until Hg(II) binds to MerR (ref. 6). Chemical nuclease studies show that the activator form, but not the repressor, induces a unique alteration of the helical structure localized at the centre of the DNA-binding site. Data presented here indicate that this Hg-MerR-induced DNA distortion corresponds to a local underwinding of the spacer region of the promoter by about 33 degrees relative to the MerR-operator complex. The magnitude and the direction of the Hg-MerR-induced change in twist angle are consistent with a positive control mechanism involving reorientation of conserved, but suboptimally phased, promoter elements and are consistent with a role for torsional stress in formation of an open complex.
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PMID:Allosteric underwinding of DNA is a critical step in positive control of transcription by Hg-MerR. 173 Dec 1

We have analysed theoretically the patterns of twist angles of B-DNA by the Tung-Harvey model mainly. It is shown that for a sequence of twist angles a smaller twist angle tends to follow a larger one and vice versa. Therefore the sequence of twist angles always takes a gentle zig-zag form. For simplicity we convert the sequence of twist angles to a symbolic sequence consisting of L and S, where L or S represents a large or a small angle, respectively. The -10 and -35 regions of 112 well-defined promoters for E. coli RNA polymerase, which were compiled by Hawley and McClure, have been analysed in terms of LS sequences in detail. The results shows that the number of LS sequences for promoters is considerably limited and the promoter mutations do not change the patterns of LS sequences in most cases. Several new ideas, which are believed to be useful in the further study, have been presented.
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PMID:Analysis of patterns of twist angles in DNA double helix. 209 3

Proton NMR spectra of the trp operator-promoter (sequence CGTACTAGTT.AACTAGTACG) show selective changes in chemical shift and relaxation rates over the range of temperature 0-45 degrees C for the non-exchangeable protons of A11 and A12 only. These bases are in the centre of the Pribnow box. The changes imply that at least three conformational states become significantly populated in this range of temperature, and probably involve a change in the propellor twists of A11 and A12 for one transition, and changes in the helical twist and local pitch for the other. As (1) mutations in the Pribnow box that destroy the TAA sequence impair promoter activity, and (2) the abortive initiation assay for RNA polymerase shows a transition near 20 degrees C, we propose that the observed conformational transitions in the trp promoter are an essential feature of good promoters.
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PMID:A temperature dependent transition in the Pribnow box of the trp promoter. 299 29

Catabolite activator protein (CAP) is a dimeric molecule (M(r) = 2 x 22,500) involved in transcription initiation of several catabolite-sensitive genes of Escherichia coli. The present communication proposes a model for the interaction of CAP with DNA. The model is based upon known geometrical features of the CAP molecule [McKay, D. B. & Steitz, T. A. (1981) Nature (London) 290, 744-749], which allow interaction between dyad-related alpha-helices of the dimeric protein and major grooves in adjacently aligned sections of right-handed B-DNA. These geometrical features suggest that in vivo CAP binding to closed-circular DNA involves CAP bridging adjacent loops of a DNA solenoidal coil. This interaction pattern is shown to be consistent with the geometrical and stoichiometric properties of nonspecifically bound CAP complexes observed by Chang et al. [Chang, J. J., Dubochet, J., Baudras, A., Blazy, B. & Takahashi, M. (1981) J. Mol. Biol. 150, 435-439]. CAP-induced coil formation is related to in vivo CAP potentiation of RNA polymerase activity in underwound closedcircular DNA. Specifically, it is proposed that CAP binding to the right-interwound form of supercoiled DNA effects a local redistribution of DNA twist-strain energy, thus resulting in the formation of a left-handed solenoidal loop. The production of this localized solenoidal loop, which reflects compensatory alterations in DNA twist and writhe, may provide a conformationally unique site for RNA polymerase binding where the DNA is partially unwound. The proposed interaction pattern is consistent with both recent DNA unwinding experiments and various nuclease protection data. Moreover, features of the model suggest that the repetitive and symmetric character of many promoter sequences may provide the structural basis for a switching mechanism operative in the differential control of gene transcription.
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PMID:A model for catabolite activator protein binding to supercoiled DNA. 675 42

Escherichia coli RNA polymerase contacts promoter DNA at two upstream regions separated by a spacer DNA. We had previously studied the effects of substitutions of simple DNA sequences in a stretch of the spacer DNA devoid of any known specific contacts with RNA polymerase. It was found that substitution of nine consecutive nonalternating dG-dC base pairs, but not nine alternating dG-dC base pairs, impaired promoter function. We proposed that this effect was due to the fact that the oligo(dG)-oligo(dC) sequence adopted a conformation (possibly A-helical) resulting in a reduction in its length and twist as compared with the B-form DNA of the alternating sequence. Here we test this hypothesis by combining the substitutions with single base pair insertions and deletions in the spacer DNA, which affect the length and the twist in known ways. Deletion and substitutions equally affect the activities of promoters with the presumed B-DNA substitutions. However, for promoters bearing the oligo(dG)-oligo(dC) substitution, a deletion in the spacer DNA impairs promoter activity to a much greater extent than the insertion of a base pair. This asymmetry is consistent with our hypothesis that the deleterious effects of the substitution are due to its having the reduced twist and/or length characteristic of A-DNA. Additionally, we present data that concern the sequence requirements for adoption of this structure that leads to reduced promoter function.
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PMID:Promoter recognition by Escherichia coli RNA polymerase. Effects of single base pair deletions and insertions in the spacer DNA separating the -10 and -35 regions are dependent on spacer DNA sequence. 851 22

Nucleotide sequences of DNA regions containing eukaryotic ribosomal promoters were analysed using strategies designed to reveal sequence-directed structural features. DNA curvature, duplex stability and pattern of twist angle variation were studied by computer modelling. Although ribosomal promoters are known to lack sequence homology (unless very closely related species are considered), investigation of these structural characteristics uncovered striking homologies in all the taxonomic groups examined so far. This wide conservation of DNA structures, while DNA sequence is not conserved, suggests that the determined structures are fundamental for ribosomal promoter function. Moreover, this result agrees well with the recent observations showing that RNA polymerase I transcription factors have not evolved as intensively as previously suspected.
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PMID:Common DNA structural features exhibited by eukaryotic ribosomal gene promoters. 871 Apr 87

We have previously demonstrated that integration host factor (IHF)-mediated activation of transcription from the ilvPG promoter of Escherichia coli requires a supercoiled DNA template and occurs in the absence of specific interactions between IHF and RNA polymerase. In this report, we describe a novel, supercoiling-dependent, DNA structural transmission mechanism for this activation. We provide theoretical evidence for a supercoiling-induced DNA duplex destabilized (SIDD) structure in the A + T-rich, ilvPG regulatory region between base pair positions +1 and -160. We show that the region of this SIDD sequence immediately upstream of an IHF binding site centered at base pair position -92 is, in fact, destabilized by superhelical stress and that this duplex destabilization is inhibited by IHF binding. Thus, in the presence of IHF, the negative superhelical twist normally absorbed by this DNA structure in the promoter distal half of the SIDD sequence is transferred to the downstream portion of the SIDD sequence containing the ilvPG promoter site. This IHF-mediated translocation of superhelical energy facilitates duplex destabilization in the -10 region of the downstream ilvPG promoter and activates transcription by increasing the rate of open complex formation.
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PMID:Activation of gene expression by a novel DNA structural transmission mechanism that requires supercoiling-induced DNA duplex destabilization in an upstream activating sequence. 969 90

Most small nuclear RNAs (snRNAs) are synthesized by RNA polymerase II, but U6 snRNA is synthesized by RNA polymerase III. In the fruit fly Drosophila melanogaster the RNA polymerase specificity of the snRNA genes is determined by a few nucleotide differences within the proximal sequence element (PSE), a conserved sequence located approximately 40-65 bp upstream of the transcription start site. The PSE is essential for transcription of both RNA polymerase II-transcribed and RNA polymerase III-transcribed snRNA genes and is recognized in Drosophila by a multi-subunit protein factor termed DM:PBP. Previous studies that employed site-specific protein-DNA photocrosslinking indicated that the conformation of the DNA-protein complex is different depending upon whether DM:PBP is bound to a U1 or U6 PSE sequence. These conformational differences of the complex probably represent an early step in determining the selection of the correct RNA polymerase. We have now obtained evidence that DM:PBP modestly bends the DNA upon interacting with the PSE and that the direction of DNA bending is similar for both the U1 and U6 PSEs. Under the assumption that DM:PBP does not significantly twist the DNA, the direction of the bend in both cases is toward the face of the DNA helix contacted by the 45 kDa subunit of DM:PBP. Together with data from partial proteolysis assays, these results indicate that the conformational differences in the complexes of DM:PBP with the U1 and U6 PSEs more likely occur at the protein level rather than at the DNA level.
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PMID:Similarities and differences in the conformation of protein-DNA complexes at the U1 and U6 snRNA gene promoters. 1090 34

We present a simple model of how local torsional stress in DNA can eject a DNA-bound protein. An estimate of the torque tau(*) required to eject a typical DNA-bound protein is made through a two-state model of the equilibrium between the bound and unbound states of the protein. For the familiar case of a nucleosome octamer bound to double-stranded DNA, we find this critical torque to be approximately equal to 9k(B)T. More weakly bound proteins and large (approximately equal to kilobase) loops of DNA are shown to be destabilized by smaller torques of only a few k(B)T. We then use our model to estimate the maximum range R(max) at which a protein can be removed by a transient source of twisting. We model twist strain propagation along DNA by simple dissipative dynamics in order to estimate R(max). Given twist pulses of the type expected to be generated by RNA polymerase and DNA gyrase, we find R(max) approximately equal to 70 and 450 bp, respectively, for critical torques of approximately equal to 2k(B)T.
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PMID:Removal of DNA-bound proteins by DNA twisting. 1173 12


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