Abstract
General stress conditions in bacterial cells cause a global cellular response called the stringent response. The first event in this control is production of large amounts of a regulatory nucleotide, guanosine-3',5'-(bis)pyrophospahte (ppGpp). It was proposed recently that ppGpp acts by decreasing stability of open complexes at promoters that make short-lived open complexes, e.g. the rRNA promoters. However, here we report that the bacteriophage lambdap(R) promoter, which forms long-lived open complexes, is inhibited by ppGpp in vitro as observed in vivo. We performed a systematic investigation of the ppGpp-specific inhibition of transcription initiation at lambdap(R) and found that ppGpp does decrease stability of open complexes at lambdap(R), but only slightly. Likewise the equilbrium binding constant and rate of open complex formation by RNA polymerase at lambdap(R) are only slightly affected by ppGpp. The major effect of ppGpp-mediated inhibition is to decrease the rate of promoter escape. We conclude that ppGpp-mediated inhibition of transcription initiation is not restricted to promoters that make short-lived open complexes. Rather we conclude that the initial catalytic step of transcript formation is affected by ppGpp, specifically formation of the first phosphodiester bond is inhibited by ppGpp at lambdap(R).
Highlights
General stress conditions in bacterial cells cause a global cellular response called the stringent response
The production of a specific nucleotide, guanosine5Ј,3Ј-(bis)pyrophosphate,1 is the primary signaling and initiating event in the stringent response. This nucleotide interacts with RNA polymerase, most likely at the interface of the  and Ј subunits [2, 3], which leads to the inhibition of synthesis of stable RNAs, and to the inhibition or activation of synthesis of specific mRNAs
Inhibition of the pR Promoter Activity by ppGpp in Vitro— Using Northern blot analysis and analysis of activity of a gene fusion consisting of the lacZ gene under control of the pR promoter, it was previously demonstrated that the bacteriophage pR promoter activity is significantly decreased during the stringent, but not relaxed, response of E. coli [13, 14, 16]
Summary
Mechanism of pR promoter inhibition by ppGpp to: 1) extend the current general mechanistic picture of ppGpp-mediated transcription inhibition and 2) to verify our previous in vivo observations with respect to ppGpp inhibition at pR, in vitro. Toward these goals we first sought to establish in vitro conditions that would reproduce the level of transcription inhibition of the pR promoter by ppGpp observed in vivo. Once optimization of in vitro conditions for ppGpp inhibition of pR were established, we proceeded to investigate the specific mechanism of ppGpp inhibition at pR
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