Growth rate-dependent control of the rrnB P1 core promoter in Escherichia coli

Bartlett, Michael S.; Gourse, Richard L.

doi:10.1128/jb.176.17.5560-5564.1994

Cited by 76 publications

(75 citation statements)

References 33 publications

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“…Although UP elements and Fis sites are required for maximal strength, rrn P1 promoters lacking these sequences (core promoters) are still regulated in response to the cell's nutritional environment (9,10). Consistent with this finding, cells lacking the fis gene regulate transcription from rrn P1 promoters similarly to wild-type strains, because feedback systems compensate for the loss of Fis (7).…”

supporting

confidence: 72%

“…ppGpp shortens the half-lives of open complexes formed at all promoters, but it only inhibits transcription from those promoters (such as rrn P1) where this step is rate-limiting (11). Strains that cannot make ppGpp exhibit relatively normal rRNA transcription during steady-state growth, in contrast to the situation during a stringent response (9,11,14).The short half-life of rrn P1 open complexes also results in a requirement in vitro for concentrations of initiating nucleoside triphosphates that are much higher than for other promoters (15). Consistent with this observation, when purine NTP concentrations are elevated in vivo by limitation for pyrimidines, rrnB P1 promoter activity increases in parallel with the ATP concentration (15).…”

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confidence: 99%

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confidence: 99%

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NTP-sensing by rRNA promoters in Escherichia coli is direct

Schneider

Gaál

Gourse

2002

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

105

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We showed previously that rrn P1 promoters require unusually high concentrations of the initiating nucleoside triphosphates (ATP or GTP, depending on the promoter) for maximal transcription in vitro. We proposed that this requirement for high initiating NTP concentrations contributes to control of the rrn P1 promoters from the seven Escherichia coli rRNA operons. However, the previous studies did not prove that variation in NTP concentration affects rrn P1 promoter activity directly in vivo. Here, we create conditions in vivo in which ATP and GTP concentrations are altered in opposite directions relative to one another, and we show that transcription from rrn P1 promoters that initiate with either ATP or GTP follows the concentration of the initiating NTP for that promoter. These results demonstrate that the effect of initiating NTP concentration on rrn P1 promoter activity in vivo is direct. As predicted by a model in which homeostatic control of rRNA transcription results, at least in part, from sensing of NTP concentrations by rrn P1 promoters, we show that inhibition of protein synthesis results in an increase in ATP concentration and a corresponding increase in transcription from rrnB P1. We conclude that translation is a major consumer of purine NTPs, and that NTP-sensing by rrn P1 promoters serves as a direct regulatory link between translation and ribosome synthesis.B ecause overexpression of ribosomes would be energetically costly, whereas underexpression would prevent the cell from taking full advantage of its nutritional environment, ribosome synthesis is regulated with the demand for protein synthesis. rRNA transcription is the rate-limiting step in ribosome synthesis in Escherichia coli and is controlled by several regulatory mechanisms acting at the level of transcription initiation (1, 2). In addition, an antitermination system ensures efficient rRNA transcription elongation (3).Each of the seven rRNA (rrn) operons in E. coli has two promoters, P1 and P2. The P1 promoters are responsible for the majority of rRNA transcription at moderate to fast growth rates and have been characterized extensively. Much of the intrinsic strength of the rrn P1 promoters results from AϩT-rich sequences (UP elements) upstream of the core promoters that recruit RNA polymerase (RNAP) to the promoter through specific interactions with the RNAP ␣-subunit (4-6). At least two trans-acting proteins affect rRNA transcription. Fis activates transcription from each of the 7 rrn P1 promoters by binding to sites upstream of Ϫ60 relative to the transcription start site, ϩ1 (4, 7), whereas H-NS contributes to repression of rrn P1 promoters during stationary phase (8).Although UP elements and Fis sites are required for maximal strength, rrn P1 promoters lacking these sequences (core promoters) are still regulated in response to the cell's nutritional environment (9, 10). Consistent with this finding, cells lacking the fis gene regulate transcription from rrn P1 promoters similarly to wild-type strains, because feedback systems comp...

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confidence: 72%

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confidence: 99%

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NTP-sensing by rRNA promoters in Escherichia coli is direct

Schneider

Gaál

Gourse

2002

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

105

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“…This contrasts with the situation at two other growth rate-regulated promoters (rrnB P1 and the leuV promoter), where GRDC does not require the UP element (2,3,29). Our results also show that, in addition to the P guaB UP element, sequences located between positions Ϫ133 and Ϫ100 are required for GRDC, and their role is to facilitate the inhibition of P guaB at lower growth rates.…”

Section: Vol 190 2008contrasting

confidence: 39%

“…Consistent with this, it has been shown that P guaB activity is subject to GRDC (8). The bestcharacterized promoter subject to GRDC that also contains an UP element is the rrnB P1 promoter, although the UP element plays no role in GRDC of this promoter (2,28). In this work, we show that the AϩT-rich sequence located upstream of the P guaB Ϫ35 region does indeed function as an UP element and that, like the rrnB P1 UP element, it contains promoter-proximal and -distal subsites that are able to activate transcription…”

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confidence: 74%

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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Stringent Control

Ishihama

2002

Encyclopedia of Molecular Biology

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Growth rate-dependent control of the rrnB P1 core promoter in Escherichia coli

Cited by 76 publications

References 33 publications

NTP-sensing by rRNA promoters in Escherichia coli is direct

NTP-sensing by rRNA promoters in Escherichia coli is direct

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

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