The effect of the DNA conformation on the rate of NtrC activated transcription of Escherichia coli RNA polymerase · σ54 holoenzyme

Journal of Molecular Biology

Volumn 300, Issue 4, 2000, Pages 709-725

  Schulz, Alexandra ^a   Langowski, Jörg ^a   Rippe, Karsten ^a  

^a GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

Author keywords

DNA curvature; DNA looping; Enhancer; Local concentration; Transcription initiation

Indexed keywords

ADENOSINE TRIPHOSPHATE; DNA; HOLOENZYME; NITROGEN REGULATORY PROTEIN C; PROTEIN C; RNA POLYMERASE; UNCLASSIFIED DRUG;

ARTICLE; COMPLEX FORMATION; DNA CONFORMATION; DNA SEQUENCE; DNA TEMPLATE; ENHANCER REGION; ESCHERICHIA COLI; GENE ACTIVATION; GENE INSERTION; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN INTERACTION; PROTEIN PHOSPHORYLATION; RNA TRANSCRIPTION;

ESCHERICHIA COLI;

EID: 0034697997     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.2000.3921     Document Type: Article

References (77)

1. Stable DNA loops in vivo and in vitro: Roles in gene regulation at a distance and in biophysical characterization of DNA
2. Going the distance: A current view of enhancer action
3. Curved DNA without A-A: Experimental estimation of all 16 DNA wedge angles
4. Upstream activator sequences are present in the promoters of nitrogen fixation genes
5. Theoretical prediction of sequence dependent DNA superstructure and their gel electrophoresis behavior
6. The intrinsic curvature of DNA in solution
7. Amino-terminal sequences of sigmaN (sigma54) inhibit RNA polymerase isomerization
8. The enhanceosome and transcriptional synergy
9. 54-dependent promoters on linear templates requires intrinsic or induced bending of the DNA
10. 54-dependent bacterial promoters
11. Recruitment of RNA polymerase is a rate-limiting step for the activation of the sigma(54) promoter Pu of pseudomonas putida
12. A and T-tract-mediated intrinsic curvature in native DNA between the binding site of the upstream activator NtrC and the nifLA promoter of Klebsiella pneumoniae facilitates transcription
13. Role of integration host factor in the regulation of the glnHp2 promoter of Escherichia coli
14. Positive and negative effects of DNA bending on activation of transcription from a distant site
15. DNA bending, flexibility, and helical repeat by cyclization kinetics
16. Structure of a B-DNA dodecamer. II. Influence of base sequence on helix structure
17. Supercoiling couples DNA curvature to the overall shape and the internal motion of the DNA molecule in solution
18. On the sequence determinants and flexibility of the kinetoplast DNA fragment with abnormal gel electrophoretic mobilities
19. DNA supercoiling and aerobic regulation of transcription from the Klebsiella pneumoniae nifLA promoter
20. Negative supercoiling induces spontaneous unwinding of a bacterial promoter
21. Transcription of the Xenopus rRNA gene promoter by its enhancer
22. A good turn for DNA: The structure of integration host factor bound to DNA
23. Role of phosphorylated metabolic intermediates in the regulation of glutamine synthetase synthesis in Escherichia coli
24. Supercoiling of intracellular DNA can occur in eukaryotic cells
25. Bending and curvature calculations in B-DNA
26. Sequence directed curvature of DNA
27. Application of the method of phage T4 DNA ligase catalyzed ring-closure to the study of DNA structure. I. Computational analysis
28. Application of the method of phage T4 DNA ligase catalyzed ring-closure to the study of DNA structure. II. NaCl dependence of DNA flexibility and helical repeat
29. The integration host factor stimulates interaction of RNA polymerase with NIFA, the transcriptional activator for nitrogen fixation operons
30. Intramolecular reaction in polycondensations. I. The theory of linear systems
31. Internal motion of supercoiled DNA: Brownian dynamics simulations of site juxtaposition
32. Modulation of intramolecular interactions in superhelical DNA by curved sequences: A Monte Carlo simulation study
33. Calibration of DNA curvature and a unified description of sequence-directed bending
34. DNA curvature influences the internal motions of supercoiled DNA
35. Curved helix segments can uniquely orient the topology of supertwisted DNA
36. Looping dynamics of linear DNA molecules and the effect of DNA curvature: A study by Brownian dynamics simulation
37. 54-dependent nifH promoter of Klebsiella pneumoniae
38. Upstream operators enhance repression of the lac-promoter
39. An enhancer stimulates transcription in trans when attached to the promoter via a protein bridge
40. Rod models of DNA: Sequence-dependent anisotropic elastic modelling of local bending phenomena
41. Initiation of transcription at the bacterial glnAp2 promoter by purified E. coli components is facilitated by enhancers
42. Superhelix organization by DNA curvature as measured through site-specific labeling
43. Mechanism of transcriptional activation by NTRC
44. DNA supercoiling and prokaryotic transcription
45. Transcriptional activation by recruitment
46. Isolation of the nitrogen assimilation regulator NRI, the product of the glnG gene of Escherichia coli
47. Transcription of glnA in E. coli is stimulated by activator bound to sites far from the promoter
48. Activation of glnA transcription by nitrogen regulator I (NRI)-phosphate in Escherichia coli: Evidence for a long-range physical interaction between NRI-phosphate and RNA polymerase
49. Binding of the transcription activator NRI (NTRC) to a supercoiled DNA segment imitates association with the natural enhancer: An electron microscopic investigation
50. Four dimers of lambda repressor bound to two suitably spaced pairs of lambda operators form octamers and DNA loops over large distances
51. Making DNA do a U-turn: IHF and related proteins
52. Crystal structure of an IHF-DNA complex: A protein-induced DNA U-turn
53. Quantitative comparison of DNA looping in vitro and in vivo: Chromatin increases effective DNA flexibility at short distances
54. Simultaneous binding of two DNA duplexes to the NtrC-enhancer complex studied by two-color fluorescence cross-correlation spectroscopy
55. Action at a distance: DNA-looping and initiation of transcription
56. Transcriptional activation via DNA-looping: Visualization of intermediates in the activation pathway of E. coli RNA polymerase-sigma 54 holoenzyme by scanning force microscopy
57. Association states of the transcription activator protein NtrC from E. coli determined by analytical ultracentrifugation
58. 54-dependent nifH promoter
59. Sequence periodicities in chicken nucleosome core DNA
60. Curvature and sequence analysis of eukaryotic promoters
61. 54 holoenzyme complexes with DNA in buffer and in air
62. Energetics of DNA twisting. I. Relation between twist and cyclization probability
63. DNA flexibility studied by covalent closure of short fragments into circles
64. DNA-looping and enhancer activity: Association between DNA-bound NtrC activator and RNA polymerase at the bacterial glnA promoter
65. The pitch of chromatin DNA is reflected in its nucleotide sequence
66. Inherently curved DNA and its structural elements
67. Conformational and thermodynamic properties of supercoiled DNA
68. The bacterial enhancer-binding protein NTRC is a molecular machine: ATP hydrolysis is coupled to transcriptional activation
69. A bacterial enhancer functions to tether a transcriptional activator near a promoter
70. Kinetics of structural changes in superhelical DNA
71. Phosphorylation of nitrogen regulator I of Escherichia coli induces strong cooperative binding to DNA essential for activation of transcription
72. 54-dependent Klebsiella pneumoniae nifL promotor in vitro
73. The locus of sequence-directed and protein-induced DNA bending