A Bacterial Enhancer Functions to Tether a Transcriptional Activator Near a Promoter

Wedel, Andrew; Weiss, David S.; Popham, David L.; Dröge, Peter; Kustu, Sydney

doi:10.1126/science.1970441

Cited by 194 publications

(136 citation statements)

References 31 publications

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“…The activator converts the closed promoter complex to an open complex that is transcriptionally competent (Sasse-Dwight and Gralla, 1988;Morett and Buck, 1989;Popham et al, 1989;Lee et al, 1993;Lee et al, 1994;Perez-Martin and de Lorenzo, 1996b). To catalyse this isomerization, the activator must hydrolyse ATP (Weiss et al, 1991;Lee et al, 1993;Lee et al, 1994;Perez-Martin and de Lorenzo, 1996b) and make productive contact with 54 -holoenzyme through a DNA loop (Buck et al, 1987;Su et al, 1990;Wedel et al, 1990). Interactions between the activator and 54 -holoenzyme are transient, and sites involved in proteinprotein interaction have not been identified in these proteins.…”

Section: Introductionmentioning

confidence: 99%

A conserved region in the σ⁵⁴‐dependent activator DctD is involved in both binding to RNA polymerase and coupling ATP hydrolysis to activation

Wang

Lee

Brewer

et al. 1997

Molecular Microbiology

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SummaryRhizobium melioti DctD activates transcription from the dctA promoter by catalysing the isomerization of closed complexes between 54 -RNA polymerase holoenzyme and the promoter to open complexes. DctD must make productive contact with 54 -holoenzyme and hydrolyse ATP to catalyse this isomerization. To define further the activation process, we sought to isolate mutants of DctD that had reduced affinities for 54 -holoenzyme. Mutagenesis was confined to the well-conserved C3 region of the protein, which is required for coupling ATP hydrolysis to open complex formation in 54 -dependent activators. Mutant forms of DctD that failed to activate transcription and had substitutions in the C-terminal half of the C3 region were efficiently cross-linked to 54 and the ␤-subunit of RNA polymerase, suggesting that they bound normally to 54 -holoenzyme. In contrast, some mutant forms of DctD with amino acid substitutions in the N-terminal half of the C3 region had reduced affinities for 54 and the ␤-subunit in the cross-linking assay. These data suggest that the N-terminal half of the C3 region of DctD contains a site that may contact 54-holoenzyme during open complex formation.

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Section: Introductionmentioning

confidence: 99%

A conserved region in the σ⁵⁴‐dependent activator DctD is involved in both binding to RNA polymerase and coupling ATP hydrolysis to activation

Wang

Lee

Brewer

et al. 1997

Molecular Microbiology

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“…To separate the polynucleotide strands of an E 54 -DNA complex requires an enhancer sequence in the DNA (42). A promoter-specific activator protein binds the enhancer to interact, by DNA looping, with holoenzyme bound at the promoter (51,62,68). Two candidate sequences, which are boxed in Fig.…”

Section: Dynamics Of Act Operon Expressionmentioning

confidence: 99%

Mutations of the Act Promoter in Myxococcus xanthus

Gronewold

Kaiser

2007

J Bacteriol

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Mutations within the ؊12 and ؊24 elements provide evidence that the act promoter is recognized by sigma-54 RNA polymerase. Deletion of the ؊20 base pair, which lies between the two conserved elements of sigma-54 promoters, decreased expression by 90%. In addition, mutation of a potential enhancer sequence, around ؊120, led to an 80% reduction in act gene expression. actB, the second gene in the act operon, encodes a sigma-54 activator protein that is proposed to be an enhancer-binding protein for the act operon. All act genes, actA to actE, are expressed together and constitute an operon, because an in-frame deletion of actB decreased expression of actA and actE to the same extent. After an initially slow phase of act operon expression, which depends on FruA, there is a rapid phase. The rapid phase is shown to be due to the activation of the operon expression by ActB, which completes a positive feedback loop. That loop appears to be nested within a larger positive loop in which ActB is activated by the C signal via ActA, and the act operon activates transcription of the csgA gene. We propose that, as cells engage in more C signaling, positive feedback raises the number of C-signal molecules per cell and drives the process of fruiting body development forward.

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“…The enhancer for this promoter, consisting of two high-affinity NtrC-binding sites, is centered at position Ϫ110 bp relative to the site of transcript initiation, but can strongly activate transcription when positioned up to at least 15 kb away in vivo (10) and up to at least 0.9 kb in vitro (11). It can also activate transcription in trans (12). NtrC is an activator that binds to the enhancer, and, when phosphorylated by NtrB protein kinase, forms higher order homo-oligomers and is capable of activating the transcription of the glnAp2 gene (13)(14)(15)(16).…”

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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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A Bacterial Enhancer Functions to Tether a Transcriptional Activator Near a Promoter

Cited by 194 publications

References 31 publications

A conserved region in the σ⁵⁴‐dependent activator DctD is involved in both binding to RNA polymerase and coupling ATP hydrolysis to activation

A conserved region in the σ⁵⁴‐dependent activator DctD is involved in both binding to RNA polymerase and coupling ATP hydrolysis to activation

Mutations of the Act Promoter in Myxococcus xanthus

DNA supercoiling allows enhancer action over a large distance

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A Bacterial Enhancer Functions to Tether a Transcriptional Activator Near a Promoter

Cited by 194 publications

References 31 publications

A conserved region in the σ54‐dependent activator DctD is involved in both binding to RNA polymerase and coupling ATP hydrolysis to activation

A conserved region in the σ54‐dependent activator DctD is involved in both binding to RNA polymerase and coupling ATP hydrolysis to activation

Mutations of the Act Promoter in Myxococcus xanthus

DNA supercoiling allows enhancer action over a large distance

Contact Info

Product

Resources

About

A conserved region in the σ⁵⁴‐dependent activator DctD is involved in both binding to RNA polymerase and coupling ATP hydrolysis to activation

A conserved region in the σ⁵⁴‐dependent activator DctD is involved in both binding to RNA polymerase and coupling ATP hydrolysis to activation