Factor Independent Activation of rrnB P1

Lin, Rongcheng; Ross, Wilma; Appleman, J. Alex; Gaál, Tamás; Leirmo, Sigrid; Schlax, Paula J.; Record, M. Thomas; Gourse, Richard L.

doi:10.1006/jmbi.1994.1098

Cited by 204 publications

(104 citation statements)

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“…Thus, the presence of an UP element in a promoter plays the major role of increasing the initial equilibrium constant of closed complex formation between RNAP and promoter DNA (13, 9). However, influences of ␣-UP element interaction on later steps in transcription initiation were also reported (13,14). The location of the UP element with respect to the transcription start site can influence the degree of transcription stimulation (15).…”

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confidence: 99%

“…It is currently believed that the transcription stimulation by an UP element has to be traced mainly to the cooperation of the sigma factor and the ␣ subunit in RNAP binding to the promoter (1,12). Thus, the presence of an UP element in a promoter plays the major role of increasing the initial equilibrium constant of closed complex formation between RNAP and promoter DNA (13,9). However, influences of ␣-UP element interaction on later steps in transcription initiation were also reported (13,14).…”

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confidence: 99%

“…The location of the UP element with respect to the transcription start site can influence the degree of transcription stimulation (15). In the Escherichia coli rrnB P1 promoter, the UP element is located in a region spanning form the Ϫ40 and Ϫ60 positions and is able to increase transcription from 30-to 70-fold (6,13). The artificial upstream re-location of the rrnB P1 UP element by a single turn of DNA helix decreases but does not prevent transcription stimulation, while further displacements abolish UP elementdependent transcription (15).…”

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Recruitment of σ54-RNA Polymerase to the Pu Promoter of Pseudomonas putida through Integration Host Factor-mediated Positioning Switch of α Subunit Carboxyl-terminal Domain on an UP-like Element

Macchi¹,

Montesissa²,

Murakami

et al. 2003

Journal of Biological Chemistry

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The interactions between the 54 -containing RNA polymerase ( 54 -RNAP) and the region of the Pseudomonas putida Pu promoter spanning from the enhancer to the binding site for the integration host factor (IHF) were analyzed both by DNase I and hydroxyl radical footprinting. A short Pu region centered at position ؊104 was found to be involved in the interaction with 54 -RNAP, both in the absence and in the presence of IHF protein. Deletion or scrambling of the ؊104 region strongly reduced promoter affinity in vitro and promoter activity in vivo, respectively. The reduction in promoter affinity coincided with the loss of IHF-mediated recruitment of the 54 -RNAP in vitro. The experiments with oriented-␣ 54 -RNAP derivatives containing bound chemical nuclease revealed interchangeable positioning of only one of the two ␣ subunit carboxylterminal domains (␣CTDs) both at the ؊104 region and in the surroundings of position ؊78. The addition of IHF resulted in perfect position symmetry of the two ␣CTDs. These results indicate that, in the absence of IHF, the 54 -RNAP asymmetrically uses only one ␣CTD subunit to establish productive contacts with upstream sequences of the Pu promoter. In the presence of IHFinduced curvature, the closer proximity of the upstream DNA to the body of the 54 -RNAP can allow the other ␣CTD to be engaged in and thus favor closed complex formation.Bacterial promoters are modular DNA regions able to establish productive interactions both with subunits of RNA polymerase holoenzyme (RNAP 1 ; subunit composition: ␣ 2 ␤␤Ј ) and regulatory proteins (1-4). The core promoter elements are signature tags for factor selectivity (4). The major sigma factor 70 generally directs RNAP to interact with the core DNA elements Ϫ10 and Ϫ35 (hexamers with consensus 5Ј-TATAAT-3Ј and 5Ј-TTGACA-3Ј, respectively) (5). The core promoter elements can be both overlapped and flanked by protein-bound DNA sites involved in the fine modulation of promoter activity (2, 4). In the last decade, a considerable amount of attention has been given to a A ϩ T-rich promoter sequence, the UP element, located upstream of the core promoter region and consisting of two distinct subsites, each of which, by itself, can be bound by the carboxyl-terminal domain of the RNAP ␣ subunit (␣CTD) (3, 6 -10). ␣CTD recognizes and interacts with the backbone structure in the minor groove of the UP element. The A ϩ T-rich sequence of the UP element are needed to provide the optimum width of minor groove for interaction with ␣CTD (7, 11). Several lines of evidence showed that the role of the UP elements is to stimulate transcription in an activator protein-independent manner and to a different extent (from 1.5 to ϳ90-fold) depending on the similarity with the consensus UP element sequence (3, 9). It is currently believed that the transcription stimulation by an UP element has to be traced mainly to the cooperation of the sigma factor and the ␣ subunit in RNAP binding to the promoter (1, 12). Thus, the presence of an UP element in a promoter plays the major ...

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Recruitment of σ54-RNA Polymerase to the Pu Promoter of Pseudomonas putida through Integration Host Factor-mediated Positioning Switch of α Subunit Carboxyl-terminal Domain on an UP-like Element

Macchi¹,

Montesissa²,

Murakami

et al. 2003

Journal of Biological Chemistry

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“…The small difference in the mobilities of the wild type and SUB fragments is likely to reflect bending, however, since the difference was greatest when the A-tract regions were near the center of the fragment ( Figure 5, PvuII or XhoI digests). Functional role of A-tracts within the UP element The UP element consists of 90% adenine and thymine residues, contains phased A/T-tracts (Figure 6), and increases transcription of rmB P1 at least 30-fold in vivo and in vitro (2,3). Replacement of the -40 to -60 region in rrnB P1 with the SUB mutation completely eliminates activation by the UP element and partially reduces activation by FIS bound at FIS Site I (3), resulting in a reduction of transcription even greater than 30-fold.…”

Section: A6 Tracts)mentioning

confidence: 99%

“…This exceptional strength results from a near consensus core promoter (-10, -35 region) activated more than 300-fold by an upstream activator region (UAR) (1)(2)(3).…”

Section: Introductionmentioning

confidence: 99%

Localization of the intrinsically bent DNA region upstream of theE.coli rrnBP1 promoter

Gaál¹,

Lin²,

Estrem³

et al. 1994

Nucl Acids Res

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DNA sequences upstream of the rrnB P1 core promoter (-10, -35 region) increase transcription more than 300-fold In vivo and in vitro. This stimulation results from a cis-acting DNA sequence, the UP element, which interacts directly with the alpha subunit of RNA polymerase, increasing transcription about 30-fold, and from a positively acting transcription factor, FIS, which increases expression another 10-fold. A DNA region exhibiting a high degree of intrinsic curvature has been observed upstream of the rrnB P1 core promoter and has thus been often cited as an example of the effect of bending on transcription. However, the precise position of the curvature has not been determined. We address here whether this bend is in fact related to activation of rRNA transcription. Electrophoretic analyses were used to localize the major bend in the rrnB P1 upstream region to position approximately -100 with respect to the transcription initiation site. Since most of the effect of upstream sequences on transcription results from DNA between the -35 hexamer and position -88, i.e. downstream of the bend center, these studies indicate that the curvature leading to the unusual electrophoretic behavior of the upstream region does not play a major role in activation of rRNA transcription. Minor deviations from normal electrophoretic behavior were associated with the region just upstream of the -35 hexamer and could conceivably influence interactions between the UP element and the alpha subunit of RNA polymerase.

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Sigma A‐bound iron–sulfur protein WhiB1 in Mycobacterium tuberculosis

Zhang

2021

Encyclopedia of Inorganic and Bioinorganic Chemistry

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WhiB1 belongs to the WhiB‐like family that is widely distributed in the phylum of Actinobacteria. It is a monomeric transcription factor that contains a [4Fe–4S] cluster in the holo‐form. In mycobacteria, the holo‐WhiB1 interacts with the domain 4 of the σ 70 ‐family primary sigma factor (σ A 4 ) in the RNA polymerase holoenzyme and plays an essential role in active cell growth. Domain 4 of the σ 70 ‐family primary sigma factors recognizes the −35 hexamer of promoter DNA and is commonly utilized by transcription factors for gene activation. However, the crystal structure of the WhiB1:σ A 4 complex reveals unexpectedly that WhiB1 binds to σ A 4 using a hydrophobic interface that differs markedly from previously characterized σ A 4 ‐bound bacterial transcription activators. Moreover, holo‐WhiB1 represses transcription by interaction with σ A 4 in vitro and WhiB1's essential role in supporting mycobacterial growth requires its interaction with σ A in vivo . Together, these results demonstrate that holo‐WhiB1 regulates gene expression by a noncanonical mechanism relative to well‐characterized σ A 4 ‐dependent transcription activators.

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Factor Independent Activation of rrnB P1

Cited by 204 publications

References 0 publications

Recruitment of σ54-RNA Polymerase to the Pu Promoter of Pseudomonas putida through Integration Host Factor-mediated Positioning Switch of α Subunit Carboxyl-terminal Domain on an UP-like Element

Recruitment of σ54-RNA Polymerase to the Pu Promoter of Pseudomonas putida through Integration Host Factor-mediated Positioning Switch of α Subunit Carboxyl-terminal Domain on an UP-like Element

Localization of the intrinsically bent DNA region upstream of theE.coli rrnBP1 promoter

Sigma A‐bound iron–sulfur protein WhiB1 in Mycobacterium tuberculosis

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