Structure and function of E. coli promoter DN

Critical Reviews in Biochemistry and Molecular Biology

Volumn 22, Issue 3, 1987, Pages 181-219

  Travers, Andrew A ^a  

^a MRC LABORATORY OF MOLECULAR BIOLOGY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; DNA DIRECTED RNA POLYMERASE; DNA DIRECTED RNA POLYMERASES;

BIOLOGICAL MODEL; CONFORMATION; ESCHERICHIA COLI; GENETIC TRANSCRIPTION; GENETICS; METABOLISM; NUCLEOTIDE SEQUENCE; PHYSIOLOGY; PROMOTER REGION; REVIEW;

BASE SEQUENCE; DNA, BACTERIAL; DNA-DIRECTED RNA POLYMERASES; ESCHERICHIA COLI; MODELS, GENETIC; NUCLEIC ACID CONFORMATION; PROMOTER REGIONS (GENETICS); TRANSCRIPTION, GENETIC;

EID: 0023473860     PISSN: 10409238     EISSN: None     Source Type: Journal    
DOI: 10.3109/10409238709101483     Document Type: Article

References (180)

1. Kinetics of open complex formation between Escherichia coli RNA polymerase and the lac UV5 promoter. Evidence for a sequential mechanism involving three step
2. Changes in the DNA structure of the lac UV5 promoter during formation of an open complex with Escherichia coli RNA polymeras
3. Temperature dependence of the rate constants of the Escherichia coli RNA polymerase-Δ PR promoter interaction. Assignment of kinetic steps corresponding to protein conformational change and DNA openin
4. Protein-nucleic acid interactions in transcription: a molecular analysi
5. Mechanism and control of transcription initiation in prokaryote
6. The regulation of transcription initiation in bacteri
7. Factor stimulating transcription by RNA polymeras
8. Bacterial DNA-dependent RNA polymerase
9. The nucleotide sequence of the cloned rpoD gene for the RNA polymerase sigma subunit from E. coli K1
10. Nucleotide sequence of the heat shock regulatory gene of E. coli suggests its protein product may be a transcription facto
11. The htpR gene product of E. coli is a sigma factor for heat shock promoter
12. Nitrogen regulation in enteric bacteri
13. Transcription of glnA by purified Escherichia coli components: core RNA polymerase and the products of glnF, glnG a
14. Two functional domains conserved in major and alternate bacterial sigma factor
15. The nucleotide sequence of the nitrogen regulation gene ntrA of Klebsiella pneumoniae and comparison with conserved features in bacterial RNA polymerase sigma factor
16. Multiple prokaryotic ribonucleic acid polymerase sigma factor
17. Small-angle X-ray study of DNA dependent RNA polymerase holoenzyme fr
18. Compilation and analysis of Escherichia coli promoter DNA sequence
19. Consensus sequence of Escherichia coli heat shock promoter
20. Regulation of nitrogen fixation gene
21. The nif promoters of Klebsiella pneumoniae have a characteristic primary structur
22. Defining a bacteriophage T4 late promoter: absence of a “-35” regio
23. Negative supercoiling induces spontaneous unwinding of a bacterial promote
24. Two RNA polymerase sigma factors from Bacillus subrilis discriminate between overlapping promoter for a developmentally regulated gen
25. Structure of the nucleosome core particle at 7 Å resolutio
26. DNA bending and its relation to nucleosome positionin
27. DNA gyrase and its complexes with DNA: direct observation by electron microscop
28. DNA structure and promoter functio
29. DNA structural variations in the E. coli tyrT promote
30. Reversible bending and helix geometry in a B-DNA dodecamer: CGCGAATTBrCGC
31. Mechanics of the sequence-dependent stacking of bases in B-DN
32. Helical periodicity of DNA determined by enzyme digestio
33. Helical repeat of DNA in solutio
34. A bent helix in kinetoplast DN
35. DNA bending at adenine-thymidine tract
36. Sequence specificity of curved DN
37. Sequence dependence of the curvature of DNA: a test of the phasing hypothesi
38. Cufved DN
39. Bent DNA for gene regulation and DNA packagin
40. Evidence for the existence of stable curvature of DNA in solutio
41. The bending of DNA in nucleosomes and its wider implication
42. Sequence periodicities in chicken nucleosome core DN
43. Structural junctions in DNA - influence of flanking sequences on nuclease digestion specificitie
44. Conformational change in the DNA associated with an unusual promoter mutation in a tRNA oper
45. DNA determinants of rRNA synthesis in E. coli: growth dependent regulation, feedback inhibition, upstream activation antiterminatio
46. Unwinding of double-stranded DNA by dehydratio
47. The genetic control of DNA supercoiling and vice vers
48. Conformational analysis of lac promoters using the nuclease activity of 1,10-phenanthroline-copper io
49. Stabilities of nearest-neighbour doublets in double-helical DNA determined by fitting calculated melting profiles to observed profile
50. Escherichia coli promoter sequences predict in vitro RNA polymerase selectivit
51. Promoters of Escherichia coli: a hierarchy of in vivo strength indicates alternate structure
52. Promoter mutations in the transfer RNA gene tyrT
53. Functional dissection of Escherichia coli promoters: information in the transcribed region is involved in late steps of the overall proces
54. The o-subunit of RNA polymerase contacts the leading ends of transcripts 9–13 bases long on the Δ PR promoter but not on T7 A
55. Initiation of DNA-dependent RNA synthesis and the effect of heparin on RNA polymeras
56. The selectivity of transcriptio
57. Rate-limiting steps in RNA chain initiatio
58. In vitro comparison of initiation properties of bacteriophage Δ wild-type PR and X3 mutant promote
59. Mechanism of activation of transcription initiation from the Δ PRM promote
60. Binding of Escherichia coli RNA polymerase holoenzyme to bacteriophage T7 DNA. Measurements of binding at bacteriophage T7 promoter A, using a template competition assa
61. Binding of Escherichia coli RNA polymerase holoenzyme to bacteriophage T7 DNA. Measurements of the rate of open complex formation at T7 promoter
62. Binding of Escherichia coli RNA polymerase holoenzyme to a bacteriophage T7 promoter containing fragment: evaluation of promoter binding constants as a function of solution condition
63. Sequence-dependent variation in the conformation of DN
64. Base sequence and helix structure variation in B and A-DN
65. A base-centered explanation of the B-to-A transition in DN
66. Deoxyribonuclease I produces staggered cuts in the DNA of chromati
67. The interaction of RNA polymerase and lac repressor with the lac control regio
68. E. coli RNA polymerase interacts homologously with two different promoter
69. The pathway of E. coli RNA polymerase-promoter complex formation as visualized by footprintin
70. Unwinding at the promoter and the modulation of transcription by DNA supercoilin
71. On the action of the cyclic AMP-cyclic AMP receptor protein complex at the Escherichia coli lactose and galactose promoter regio
72. Rapid “footprinting” on supercoiled DN
73. Characterisation of the B-lactamase promoter of pBR32
74. RNA polymerase interactions with the upstream region of the tyrT promote
75. Nucleotide sequence of the promoter region of the gene cluster for the proton-translocating ATPase from Escherichia coli and identification of the active promote
76. Mechanism of activation of transcription by the complex formed between cyclic AMP and its recepto
77. Topography of interaction of Escherichia coli RNA polymerase subunits with the lacUV5 promote
78. The selection and characterisation of two novel mutations in the overlapping promoters of the Escherichia coli galactose opero
79. Promoter recognition by Escherichia coli RNA polymerase. Effects of substitutions in the spacer DNA separating the -10 and -35 region
80. DNA conformation at the 5′ end of the chicken adult β-globin gen
81. Conformation of promoter DNA: fine mapping of S1 hypersensitive site
82. Homocopolymer sequences in the spacer of a sea urchin histone gene repeat are sensitive to S1 nucleas
83. A structural basis for S1 nuclease sensitivity of double stranded DN
84. Nucleosome cores reconstituted from poly (dA-dT) and the octamer of histone
85. Chromatin and core particles formed from the inner histones and synthetic polydeoxynucleotides of defined sequenc
86. Physiochemical studies on the interactions between DNA and RNA polymerase. Unwinding of the DNA helix by Escherichia coli RNA polymeras
87. A topological model for transcription based on unwinding angle analysis of E. coli RNA polymerase binary initiation and ternary complexe
88. High-resolution analysis of lac transcription complexes inside cell
89. Effect of superhelicity on the transcription from the tet promoter of pB322. Abortive initiation and unwinding experiment
90. A new experimental approach for studying the association between RNA polymerase and the tet promoter of pB32
91. Intermediates in transcription initiation from the E. colt lac UV5 promote
92. Supercoiling response of the lac p' promot
93. DNA supercoiling affects in vitro transcription of two maize chloroplast genes differentl
94. Characterisation in vitro of the effect of spacer length on the activity of Escherichia coli RNA polymerase at the TAC promote
95. Mechanism of CRP-cAMP activation of lac operon transcription initiation activation of the P1 promote
96. Effect of supercoiling on the abortive initiation kinetics of the RNA-I promoter of Col El plasmid DN
97. The lac promoter: a functional hybrid derived from the trp and lac promoter
98. Ion effects on the aggregation and DNA binding reactions of Escherichia coli RNA polymeras
99. Selective inhibition of tRNAtyr' transcription by guanosine 3′ diphosphate 5′-diphosphat
100. Selectivity of RNA chain initiation in vitro. III. Variables affecting initiation of transcriptio
101. Supercoiling response of a bacterial tRNA gen
102. Formylmethionyl-tRNA alters RNA polymerase specificit
103. On the nature of DNA promoter conformations: the effects of glycerol and dimethylsul-phoxid
104. Activation of transcription at specific promoters by glycero
105. An Escherichia coli RNA polymerase tight-binding site on T7 DNA is a weak promoter subject to substrate inhibitio
106. Bacterial regulation: global regulatory network
107. Stringent control of bacterial transcriptio
108. The stringent respons
109. rpoB mutation in Escherichia coli alters control of ribosome synthesis by guanosine tetraphosphat
110. Relaxed mutants of Escherichia coli RNA polymeras
111. Genetic studies on the B subunit of Escherichia coli RNA polymerase. VII. RNA polymerase is a target for ppGp
112. A mutation affecting the subunit of RNA polymerase changes transcriptional specificit
113. Promoter sequence for the stringent control of bacterial ribonucleic acid synthesi
114. Conserved features of coordinately regulated E. coli promoter
115. The synthesis and cloning of two tyrosine suppressor tRNA genes with altered promoter sequence
116. Genetically separable functional elements mediate the optimal transcription and stringent regulation of a bacterial tRNA gen
117. A tRNAtyr promoter with an altered response to ppGpp
118. Regulation of the expression of the tufB operon: DNA sequences directly involved in the stringent contro
119. Differential stringent control of the tandem E. coli ribosomal RNA promoters from the rrnA operon expressed in vivo in multicopy plasmid
120. Identification of initiation sites for the in vitro transcription of rRNA opcrons rrnE and rrnA
121. Effect of deletions near Escherichia coli rrn promoter P2 on inhibition of in vitro transcription by guanosine tetraphosphat
122. Promoter selectivity of Escherichia coli RNA polymerase: differential stringent control of the multiple promoters from ribosomal RNA and protein operon
123. The molecular topography of RNA polymerase-promoter interactio
124. The regulation of RNA polymerase by guanosine 5′ diphosphate 3′ diphosphat
125. Specific inhibition of ribosomal RNA synthesis in vitro by guanosine 3′ diphosphate 5′ diphosphat
126. Modulation of RNA polymerase specificity by ppGp
127. Vitro transcription of three different ribosomal RNA cistrons of E. coli: heterogeneity of control region
128. Selective inhibition of transcription of the E. coli tufB operon by guanosine-5′-diphosphate-3′-diphosphat
129. Interaction of ppGpp structural analogs with RNA polymeras
130. Aggregation equilibria of Escherichia coli RNA polymerase: evidence for anion-linked conformational transitions in the promoters of core and holoenzyme
131. Evidence for a specific association between RNA polymerase subunits O and β involved in the closed to open complex transitio
132. Functional heterogeneity of Escherichia coli ribon-ucleic acid polymerase holoenzym
133. Some physical properties of RNA polymeras
134. Repressor structure and the mechanism of positive contro
135. Positive control of transcription initiation in Escherichia coli. A base substitution at the Pribnow box render ompF expression independent of a positive regulato
136. Positive regulation in bacteri
137. Bacteriophage Δ protein cII binds promoters on the opposite face of the DNA helix from RNA polymeras
138. Differential effects of mutations on discrete steps in transcription initiation at the A PRE promote
139. The effect of a lambda repressor mutation on the activation of transcription initiation from the lambda PRM promote
140. Binding of CRP to DNA-dependent RNA polymerase from E. coli: modulation by CAMP of the interactions with free and DNA bound holo and core enzym
141. The locus of sequence-directed and protein induced DNA bendin
142. A dimer of AraC protein contacts three adjacent major groove regions of the aral DNA sit
143. Mutations affecting regulation of Klebsiella pneumoniae nifH (nitro-genase reductase) promote
144. Upstream activator sequences are present in the promoters of nitrogen fixation gene
145. Transcription of glnA in E. coli is stimulated by an activator bound to sites far from the promote
146. An operator at -280 bp that is required for the repression of araBAD operon promoter: addition of DNA helical turns between the operator and promoter cyclically hinders repressio
147. Gene regulation by proteins acting nearby and at a distanc
148. The control of stable RNA synthesis in bacteri
149. Requirement for an upstream element for optimal transcription of a bacterial tRNA gen
150. Alteration of the growth rate dependent regulation of Escherichia coli tyrT expression by promoter mutation
151. ppGpp regulates the binding of two RNA polymerase molecules to the tyrT promote
152. Regulation of the kinetics of the interaction of Escherichia coli RNA polymerase with the lambda PR promoter by salt concentratio
153. Dependence of the putrecine content of Escherichia coli on the osmotic strength of the mediu
154. Role of amino acids in osmoregulation of non-holophilic bacteri
155. Equilibrium DNA binding of AraC protein: compensation for displaced ion
156. Cruciform formation in negatively supercoiled DNA may be kinetically forbidden under physiological condition
157. Control of rRNA and tRNA synthesis in Escherichia coli by guanosine tetraphosphat
158. Synthesis and activity of ribonucleic acid polymerase
159. Establishment of exponential growth after a nutritional shift-up in Escherichia coli B/r: accumulation of deoxyribonucleic acid, ribonucleic acid and protei
160. The mechanism of RNA polymerase activation at the lambda PRM and lac P+ promoter
161. The general affinity of lac repressor for E. coli DNA: implications for gene regulation in procaryotes and eukqote
162. Functional interrelationship between two tandem E. coli ribosomal RNA promoter
163. Dependency on medium and temperature on cell size and chemical composition during balanced growth
164. An analysis of bacterial growt
165. Regulation of the synthesis of ribosomes and ribosomal component
166. Formyl-methonyl-tRNA alters RNA polymerase specificit
167. Promoter selectivity of Escherichia coli RNA polymerase: alteration by fMet-tRNAfMe