Journal article Open Access

Bacterial promoter architecture: subsite structure of UP elements and interactions with the carboxy-terminal domain of the RNA polymerase alpha subunit

Estrem, S. T.; Ross, W.; Gaal, T.; Chen, Z. W. S.; Niu, W.; Ebright, R. H.; Gourse, R. L.


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    "description": "We demonstrate here that the previously described bacterial promoter upstream element (UP element) consists of two distinct subsites, each of which, by itself, can bind the RNA polymerase holoenzyme \u03b1 subunit carboxy-terminal domain (RNAP \u03b1CTD) and stimulate transcription. Using binding-site-selection experiments, we identify the consensus sequence for each subsite. The selected proximal subsites (positions \u221246 to \u221238; consensus 5\u2032-AAAAAARNR-3\u2032) stimulate transcription up to 170-fold, and the selected distal subsites (positions \u221257 to \u221247; consensus 5\u2032-AWWWWWTTTTT-3\u2032) stimulate transcription up to 16-fold. RNAP has subunit composition \u03b12\u03b2\u03b2\u2032\u03c2 and thus contains two copies of \u03b1CTD. Experiments with RNAP derivatives containing only one copy of \u03b1CTD indicate, in contrast to a previous report, that the two \u03b1CTDs function interchangeably with respect to UP element recognition. Furthermore, function of the consensus proximal subsite requires only one copy of \u03b1CTD, whereas function of the consensus distal subsite requires both copies of \u03b1CTD. We propose that each subsite constitutes a binding site for a copy of \u03b1CTD, and that binding of an \u03b1CTD to the proximal subsite region (through specific interactions with a consensus proximal subsite or through nonspecific interactions with a nonconsensus proximal subsite) is a prerequisite for binding of the other \u03b1CTD to the distal subsite.", 
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    "title": "Bacterial promoter architecture: subsite structure of UP elements and interactions with the carboxy-terminal domain of the RNA polymerase alpha subunit", 
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