Promoter Recognition (promoter + recognition)

Distribution by Scientific Domains

Selected Abstracts

The interaction between ,S, the stationary phase , factor, and the core enzyme of Escherichia coli RNA polymerase

GENES TO CELLS, Issue 3 2002
Frédéric Colland
Background: The RNA polymerase holoenzyme of Escherichia coli is composed of a core enzyme (subunit structure ,2,,,) associated with one of the , subunits, required for promoter recognition. Different , factors compete for core binding. Among the seven , factors present in E. coli, ,70 controls gene transcription during the exponential phase, whereas ,S regulates the transcription of genes in the stationary phase or in response to different stresses. Using labelled ,S and ,70, we compared the affinities of both , factors for core binding and investigated the structural changes in the different subunits involved in the formation of the holoenzymes. Results: Using native polyacrylamide gel electrophoresis, we demonstrate that ,S binds to the core enzyme with fivefold reduced affinity compared to ,70. Using iron chelate protein footprinting, we show that the core enzyme significantly reduces polypeptide backbone solvent accessibility in regions 1.1, 2.5, 3.1 and 3.2 of ,S, while increasing the accessibility in region 4.1 of ,S. We have also analysed the positioning of ,S on the holoenzyme by the proximity-dependent protein cleavage method using ,S derivatives in which FeBABE was tethered to single cysteine residues at nine different positions. Protein cutting patterns are observed on the , and ,, subunits, but not ,. Regions 2.5, 3.1 and 3.2 of ,S are close to both , and ,, subunits, in agreement with iron chelate protein footprinting data. Conclusions: A comparison between these results using ,S and previous data from ,70 indicates similar contact patterns on the core subunits and similar characteristic changes associated with holoenzyme formation, despite striking differences in the accessibility of regions 4.1 and 4.2. [source]

MicroReview: Archaeal transcription and its regulators

E. Peter Geiduschek
Summary The relatively complex archaeal RNA polymerases are constructed along eukaryotic lines, and require two initiation factors for promoter recognition and specific transcription that are homologues of the RNA polymerase II TATA-binding protein and TFIIB. Many archaea also produce histones. In contrast, the transcriptional regulators encoded by archaeal genomes are primarily of bacterial rather than eukaryotic type. It is this combination of elements commonly regarded as separate and mutually exclusive that promises unifying insights into basic transcription mechanisms across all three domains of life. [source]

Region 4 of , as a target for transcription regulation

Simon L. Dove
Summary Bacterial , factors play a key role in promoter recognition, making direct contact with conserved promoter elements. Most , factors belong to the ,70 family, named for the primary , factor in Escherichia coli. Members of the ,70 family typically share four conserved regions and, here, we focus on region 4, which is directly involved in promoter recognition and serves as a target for a variety of regulators of transcription initiation. We review recent advances in the understanding of the mechanism of action of regulators that target region 4 of ,. [source]

UPs and downs in bacterial transcription initiation: the role of the alpha subunit of RNA polymerase in promoter recognition

Richard L. Gourse
In recent years, it has become clear that promoter recognition by bacterial RNA polymerase involves interactions not only between core promoter elements and the , subunit, but also between a DNA element upstream of the core promoter and the , subunit. DNA binding by , can increase transcription dramatically. Here we review the current state of our understanding of the , interaction with DNA during basal transcription initiation (i.e. in the absence of proteins other than RNA polymerase) and activated transcription initiation (i.e. when stimulated by transcription factors). [source]