UP element-dependent transcription at the Escherichia coli rrnB P1 promoter: positional requirements and role of the RNA polymerase alpha subunit linker

Meng, Wenmao; Belyaeva, Tamara A.; Savery, Nigel J.; Busby, Stephen J. W.; Ross, Wilma; Gaál, Tamás; Gourse, Richard L.; Thomas, Mark S.

doi:10.1093/nar/29.20.4166

Cited by 34 publications

(36 citation statements)

References 59 publications

(102 reference statements)

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“…This can be explained by the rationale that a decrease in the activity of the putative UP element in the presence of ␣265A leads to a compensatory increase in transcription from core P guaB . The effect of the mutant ␣ on UP element function was therefore quantified as described previously (13,24,33). Thus, in the presence of ␣265A, the stimulation of P guaB due to the putative UP element was reduced by a factor of ϳ2.5 (from 9.5-fold to 3.6-fold) (see Fig.…”

Section: Vol 190 2008 the Guab Promoter Up Element 2453mentioning

confidence: 99%

The UP Element Is Necessary but Not Sufficient for Growth Rate-Dependent Control of the Escherichia coli guaB Promoter

Husnain

Thomas

2008

J Bacteriol

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The Escherichia coli guaB promoter (P guaB ) regulates the transcription of two genes, guaB and guaA, that are required for de novo synthesis of GMP, a precursor for the synthesis of guanine nucleoside triphosphates. The activity of P guaB is subject to growth rate-dependent control (GRDC). Here we show that the A؉T-rich sequence located between positions ؊59 and ؊38 relative to the guaB transcription start site stimulates transcription from P guaB ϳ8-to 10-fold and, in common with other UP elements, requires the C-terminal domain of the RNA polymerase ␣ subunit for activity. Like the rrnB P1 UP element, the P guaB UP element contains two independently acting subsites located at positions ؊59 to ؊47 and ؊46 to ؊38 and can stimulate transcription when placed upstream of the lacP1 promoter. We reveal a novel role for the P guaB UP element by demonstrating that it is required for GRDC. The involvement of the UP element in GRDC also requires the participation of sequences located at least 100 bp upstream of the guaB transcription start site. These sequences are required for down-regulation of P guaB activity at lower growth rates.Escherichia coli RNA polymerase (RNAP) is a multisubunit complex consisting of an ␣ subunit homodimer, single ␤, ␤Ј, and subunits, and one of several subunits (14). The ␣ subunit contains an N-terminal domain (␣NTD; residues 8 to 232) and a C-terminal domain (␣CTD; residues 249 to 329) (5, 21, 44). ␣NTD and ␣CTD are separated by a flexible linker that is at least 13 amino acids long (5,20,25). ␣CTD plays important roles in transcription activation by contacting a number of transcription factors (6, 18) or through interacting with an AϩT-rich DNA sequence referred to as the UP element (16).UP elements stimulate transcription by recruiting ␣CTD to DNA (32, 43). The best-studied UP element spans the region from Ϫ59 to Ϫ38 at the rrnB P1 promoter (16). The rrnB P1 UP element contains two domains, a ϳ9-bp proximal UP element subsite located at positions Ϫ46 to Ϫ38 and a ϳ13-bp distal UP element subsite located at positions Ϫ59 to Ϫ47. Each subsite functions independently by recruiting one ␣CTD (11). The amino acid residues in ␣CTD that comprise the 265 determinant, including residues V264, R265, N268, N294, G296, K298, and S299, interact with UP element and A-tract sequences by contacting the DNA backbone, and R265 makes additional contacts with bases in the minor groove (4, 32, 43). These residues are the most important for rrnB P1 UP element utilization both in vivo and in vitro (13, 35). In the absence of a strong distal UP element subsite, ␣CTD bound to a consensus or near-consensus proximal UP element subsite also makes productive contacts with region 4.2 of 70 that serve to stimulate transcription (7,35).The E. coli guaB promoter (P guaB ) regulates the transcription of two genes, guaB and guaA, which together constitute the guaBA operon. The guaB and guaA genes encode IMP dehydrogenase and GMP synthetase, respectively, and are required for the biosynthesis of GMP from IMP (22, 42). P guaB...

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Section: Vol 190 2008 the Guab Promoter Up Element 2453mentioning

confidence: 99%

The UP Element Is Necessary but Not Sufficient for Growth Rate-Dependent Control of the Escherichia coli guaB Promoter

Husnain

Thomas

2008

J Bacteriol

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“…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). The ability of ␣CTD to contact DNA and/or activator molecules at different locations upstream of the core promoter (8,(15)(16)(17)(18)(19)(20)(21) has been attributed to the flexibility of the linker connecting ␣CTD to the ␣ amino-terminal domain (␣NTD) (8,22) assembled in the body of RNAP. This linker flexibility also accounts for the ability of the two copies of ␣CTD to function interchangeably with respect to the subsite recognition within the UP element (10).…”

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confidence: 99%

“…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). 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).…”

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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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“…In E. coli the A ϩ T-rich UP elements binding the C-terminal domain of the RNAP ␣ subunit are normally located between positions Ϫ40 and Ϫ60 from the transcription start point (48). At fisP1 a sequence between positions Ϫ52 and Ϫ39 ( Ϫ52 ATTGGTCAAAGTTT Ϫ39 ) could serve as a presumptive proximal UP element-like subsite, but this is unlikely because the substitutions of Gs for Ts and Cs for As in this sequence in FIGURE 8.…”

Section: Relevance Of the Upstream Rnap Binding And The Spatial Arranmentioning

confidence: 99%

Upstream Binding of Idling RNA Polymerase Modulates Transcription Initiation from a Nearby Promoter

Gerganova

Maurer

Stoliar

et al. 2015

Journal of Biological Chemistry

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Background:The fis promoter upstream region harbors RNA polymerase binding sites of unknown function. Results: Modifications of the upstream polymerase binding affect fis gene expression in a supercoiling-dependent manner. Conclusion: Concomitant binding of RNA polymerase at the fis promoter and upstream region acts as a topological device regulating transcription. Significance: RNA polymerase can act as an architectural factor modulating the activity of transcription initiation complexes.

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UP element-dependent transcription at the Escherichia coli rrnB P1 promoter: positional requirements and role of the RNA polymerase alpha subunit linker

Cited by 34 publications

References 59 publications

The UP Element Is Necessary but Not Sufficient for Growth Rate-Dependent Control of the Escherichia coli guaB Promoter

The UP Element Is Necessary but Not Sufficient for Growth Rate-Dependent Control of the Escherichia coli guaB Promoter

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

Upstream Binding of Idling RNA Polymerase Modulates Transcription Initiation from a Nearby Promoter

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