Promoter opening by ς<sup>54</sup> and ς<sup>70</sup> RNA polymerases: ς factor-directed alterations in the mechanism and tightness of control

Guo, Yanjie; Lew, Chih M.; Gralla, Jay D.

doi:10.1101/gad.794800

Cited by 67 publications

(90 citation statements)

References 49 publications

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“…It has been shown that NtrC can stimulate binding of purified 54 subunit to ''fork junction'' (partially single-stranded) promoter DNA in the absence of ATP (29), implying that NtrC could possibly communicate with the closed complex even without ATP. However preincubation of all components (core polymerase, promoter DNA, NtrC, NtrB, and 54 ) for different times without ATP did not change the rate of transcription initiation on either relaxed or sc DNA with 2.5-kb spacing (data not shown).…”

Section: Dna Supercoiling Greatly Facilitates Enhancer-promoter Communi-mentioning

confidence: 99%

DNA supercoiling allows enhancer action over a large distance

Liu

Бондаренко

Ninfa

et al. 2001

Proc. Natl. Acad. Sci. U.S.A.

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Enhancers are regulatory DNA elements that can activate their genomic targets over a large distance. The mechanism of enhancer action over large distance is unknown. Activation of the glnAp2 promoter by NtrC-dependent enhancer in Escherichia coli was analyzed by using a purified system supporting multiple-round transcription in vitro. The data suggest that DNA supercoiling is an essential requirement for enhancer action over a large distance (2,500 bp) but not over a short distance (110 bp). DNA supercoiling facilitates functional enhancer-promoter communication over a large distance, probably by bringing the enhancer and promoter into close proximity.T ranscriptional enhancers are relatively short (30 -200 bp) DNA sequences usually composed of several binding sites for activator protein(s). The landmark of enhancers is their ability to communicate with promoters and activate genes over a large distance (up to 60 kb; see ref. 1 for a review). Prokaryotic and eukaryotic enhancers share several key properties such as ability to activate transcription over a large distance, tight coupling of DNA melting with ATP hydrolysis and high stability of the initiation complexes (see refs. 2 and 3 for recent reviews). In contrast to eukaryotic enhancers, prokaryotic enhancers can activate transcription over a large distance in vitro. This ability allows detailed analysis of the mechanism of enhancer action impossible in the case of eukaryotic enhancers.The mechanism of enhancer action over a large distance is unknown. It is most likely that proteins bound at the enhancer and promoter directly interact such that intervening DNA forms a loop (see refs. 4 and 5 for reviews). The main problem for communication over a large distance is low concentration of the DNA regions in the vicinity of each other (see ref. 4 for a review). Measurements of local concentration of linear DNA ends in the vicinity of each other suggest that it is relatively high (10 Ϫ7 M) only when the distance between DNA ends is 100-900 bp (6). When distance between the DNA ends is increased to 3 kb, their local concentration is decreased by an order of magnitude (6). Thus, it is remarkable that DNA regions positioned far away from each other (such as an enhancer and a promoter) can communicate efficiently.Several models have been proposed to explain the mechanism of enhancer action over a large distance. One class of models suggests that initial communication of an enhancer with a promoter leads to formation of a stable DNA-protein complex in the vicinity of the promoter. This stable complex may facilitate subsequent rounds of transcription serving as a ''memory'' of initial enhancer-promoter interaction (see ref. 1 for a review). Alternatively, the average distance between promoter and enhancer could be considerably decreased if the intervening DNA is supercoiled (sc) or bent (see ref. 4 for a review). It has also been shown that sequence-dependent superhelical DNA inserts can facilitate enhancer action (7).The mechanism of action of the NtrC-dependent, 54...

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Section: Dna Supercoiling Greatly Facilitates Enhancer-promoter Communi-mentioning

confidence: 99%

DNA supercoiling allows enhancer action over a large distance

Liu

Бондаренко

Ninfa

et al. 2001

Proc. Natl. Acad. Sci. U.S.A.

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“…Shift Assay-Recently, we developed a band shift assay in which sigma 54 holoenzyme-DNA complexes change their mobility in response to added activator (10). The altered complex appears not to contain activator but rather to represent an activatorinduced conformational change (6,10,11).…”

Section: Effect Of Mutation On Response To Activator In a Bandmentioning

confidence: 99%

“…Interaction at this fork is repressive in the sense that the conformation of sigma bound to it helps keep the holoenzyme silent by blocking its ability to melt DNA. Activators can overcome this silencing by triggering conformational changes in both sigma and holoenzyme (6,10,11). Both the silent state and the active state rely on a complex network of interactions that centrally involve the promoter Ϫ12 element (9,(13)(14)(15).…”

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confidence: 99%

Roles for the C-terminal Region of Sigma 54 in Transcriptional Silencing and DNA Binding

Wang

Gralla

2001

Journal of Biological Chemistry

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Twenty-one conserved positively charged and aromatic amino acids between residues 331 and 462 of sigma 54 were changed to alanine, and the mutant proteins were studied by transcription, band shift analysis, and footprinting in vitro. A small segment corresponding to the rpoN box was found to be most important for binding duplex DNA. Two amino acids, 52 residues apart, were found to be critical for maintaining transcriptional silencing in the absence of activator. These two activator bypass mutants and several other mutants failed to bind the type of fork junction DNA thought to be required to maintain silencing. The two bypass mutants showed a binding pattern to DNA probes that was unique, both in comparison to other C-terminal mutants and to previously known N-terminal bypass mutants. On this basis, a model is proposed for the role of the C terminus and the N terminus of sigma 54 in enhancerdependent transcription.

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“…Initiation of s 54 -RNAP-dependent transcription resembles eukaryotic transcription initiation by RNAP II. (Guo et al, 1999(Guo et al, , 2000Fu et al, 2000). A closed complex of s class I -RNAP-promoter isomerizes spontaneously to the active, open complex.…”

Section: Introductionmentioning

confidence: 99%

“…Contact between the activator and the s 54 -RNAP-promoter complex is achieved by DNA looping, facilitated either by the integration host factor (IHF) protein or by intrinsic DNA topology (Pérez-Martin et al, 1994;Carmona et al, 1997). Control, imposed on the DNA melting step, requires ATP hydrolysis and involves the promoter 212/211 element (Guo et al, 1999(Guo et al, , 2000 bound inside the RNAP channel (Polyakov et al, 1995;Zhang et al, 1999;Severinov, 2000;Foster et al, 2001). …”

Section: Introductionmentioning

confidence: 99%

A σ 54-dependent promoter in the regulatory region of the Escherichia coli rpoH gene

et al. 2007

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The Escherichia coli rpoH gene is transcribed from four known and differently regulated promoters: P1, P3, P4 and P5. This study demonstrates that the conserved consensus sequence of the s 54 promoter in the regulatory region of the rpoH gene, described previously, is a functional promoter, P6. The evidence for this conclusion is: (i) the specific binding of the s 54 -RNAP holoenzyme to P6, (ii) the location of the transcription start site at the predicted position (C, 30 nt upstream of ATG) and (iii) the dependence of transcription on s 54 and on an ATP-dependent activator. Nitrogen starvation, heat shock, ethanol and CCCP treatment did not activate transcription from P6 under the conditions examined. Two activators of s 54 promoters, PspF and NtrC, were tested but neither of them acted specifically. Therefore, PspFDHTH, a derivative of PspF, devoid of DNA binding capability but retaining its ATPase activity, was used for transcription in vitro, taking advantage of the relaxed specificity of ATP-dependent activators acting in solution. In experiments in vivo overexpression of PspFDHTH from a plasmid was employed. Thus, the s 54 -dependent transcription capability of the P6 promoter was demonstrated both in vivo and in vitro, although the specific conditions inducing initiation of the transcription remain to be elucidated. The results clearly indicate that the closed s 54 -RNAP-promoter initiation complex was formed in vitro and in vivo and needed only an ATP-dependent activator to start transcription.

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Promoter opening by ς⁵⁴ and ς⁷⁰ RNA polymerases: ς factor-directed alterations in the mechanism and tightness of control

Cited by 67 publications

References 49 publications

DNA supercoiling allows enhancer action over a large distance

DNA supercoiling allows enhancer action over a large distance

Roles for the C-terminal Region of Sigma 54 in Transcriptional Silencing and DNA Binding

A σ 54-dependent promoter in the regulatory region of the Escherichia coli rpoH gene

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Promoter opening by ς54 and ς70 RNA polymerases: ς factor-directed alterations in the mechanism and tightness of control

Cited by 67 publications

References 49 publications

DNA supercoiling allows enhancer action over a large distance

DNA supercoiling allows enhancer action over a large distance

Roles for the C-terminal Region of Sigma 54 in Transcriptional Silencing and DNA Binding

A σ 54-dependent promoter in the regulatory region of the Escherichia coli rpoH gene

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Promoter opening by ς⁵⁴ and ς⁷⁰ RNA polymerases: ς factor-directed alterations in the mechanism and tightness of control