scholarly journals Fine structure of E. coli RNA polymerase-promoter interactions: alpha subunit binding to the UP element minor groove

2001 ◽  
Vol 15 (5) ◽  
pp. 491-506 ◽  
Author(s):  
W. Ross
Keyword(s):  
Fine Structure ◽  
Rna Polymerase ◽  
Minor Groove ◽  
Alpha Subunit ◽  
E Coli ◽  
Rna Polymerase Promoter

Interaction of the C-terminal domain of the E. coli RNA polymerase α subunit with the UP element: recognizing the backbone structure in the minor groove surface11Edited by R. Ebright

2001 ◽  
Vol 306 (2) ◽  
pp. 213-225 ◽  
Author(s):  
Kazuhiro Yasuno ◽  
Toshio Yamazaki ◽  
Yoshiyuki Tanaka ◽  
Takashi S Kodama ◽  
Akimasa Matsugami ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Minor Groove ◽  
Α Subunit ◽  
E Coli ◽  
Terminal Domain ◽  
Backbone Structure

scholarly journals Novel tools for the prediction of promoters in plants and bacteria

1970 ◽  
pp. 351-355
Author(s):  
I. A. Shahmuradov
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Sigma Factors ◽  
Promoter Prediction ◽  
Transcription Start ◽  
Transcription Start Sites ◽  
Computer Tools ◽  
E Coli ◽  
Prediction Program ◽  
Rna Polymerase Promoter

Aim. The computational search for promoters remains an attractive problem in bioinformatics. Despite the attention it has received for many years, the problem has not been addressed satisfactorily. These studies were aimed to develop novel computer tools for prediction of promoters (transcription start sites, TSSs) in plants and bacteria. Results. Two novel tools for prediction of RNA polymerase II promoters in plants (TSSPlant) and bacteria (bTSSfinder) have been developed. TSSPlant achieves significantly higher accuracy compared to the next best promoter prediction program for both TATA and TATA-less promoters; it is available to download as a standalone program at http://www.cbrc.kaust.edu.sa/download/. bTSSfinder predicts promoters for five classes of σ factors in Cyanobacteria (σA, σC, σH, σG and σF) and for five classes of sigma factors in E. coli (σ70, σ38, σ32, σ28 and σ24). Comparing to currently available tools, bTSSfinder achieves highest accuracy. bTSSfinder is available standalone and online at http://www.cbrc.kaust.edu.sa/btssfinder. Conclusions. To date, TSSPlant and bTSSfinder are most accurate promoter predictors in plants and bacteria, respectively. Keywords: transcription, RNA polymerase, promoter, TSS, promoter prediction.

scholarly journals The transcriptional activator of the bfp operon in EPEC (PerA) interacts with the RNA polymerase alpha subunit

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Cristina Lara-Ochoa ◽  
Fabiola González-Lara ◽  
Luis E. Romero-González ◽  
Juan B. Jaramillo-Rodríguez ◽  
Sergio I. Vázquez-Arellano ◽  
...  
Keyword(s):  
Amino Acids ◽  
Rna Polymerase ◽  
Virulence Genes ◽  
Phenotypic Expression ◽  
In Silico Analysis ◽  
Alpha Subunit ◽  
E Coli ◽  
Enterocyte Effacement ◽  
Silico Analysis ◽  
Activate Gene

AbstractEnteropathogenic E. coli virulence genes are under the control of various regulators, one of which is PerA, an AraC/XylS-like regulator. PerA directly promotes its own expression and that of the bfp operon encoding the genes involved in the biogenesis of the bundle-forming pilus (BFP); it also activates PerC expression, which in turn stimulates locus of enterocyte effacement (LEE) activation through the LEE-encoded regulator Ler. Monomeric PerA directly binds to the per and bfp regulatory regions; however, it is not known whether interactions between PerA and the RNA polymerase (RNAP) are needed to activate gene transcription as has been observed for other AraC-like regulators. Results showed that PerA interacts with the alpha subunit of the RNAP polymerase and that it is necessary for the genetic and phenotypic expression of bfpA. Furthermore, an in silico analysis shows that PerA might be interacting with specific alpha subunit amino acids residues highlighting the direction of future experiments.

RNA polymerase: Preparation and structural analysis of helical polymers

1984 ◽  
Vol 42 ◽  
pp. 152-153
Author(s):  
E. Loren Buhle ◽  
Pamela Rew ◽  
Ueli Aebi
Keyword(s):  
Structural Analysis ◽  
Rna Polymerase ◽  
Molecular Level ◽  
X Ray Diffraction ◽  
Helical Polymers ◽  
X Ray ◽  
E Coli ◽  
The Past ◽  
Ordered Arrays ◽  
Low Ionic Strength

While DNA-dependent RNA polymerase represents one of the key enzymes involved in transcription and ultimately in gene expression in procaryotic and eucaryotic cells, little progress has been made towards elucidation of its 3-D structure at the molecular level over the past few years. This is mainly because to date no 3-D crystals suitable for X-ray diffraction analysis have been obtained with this rather large (MW ~500 kd) multi-subunit (α2ββ'ζ). As an alternative, we have been trying to form ordered arrays of RNA polymerase from E. coli suitable for structural analysis in the electron microscope combined with image processing. Here we report about helical polymers induced from holoenzyme (α2ββ'ζ) at low ionic strength with 5-7 mM MnCl2 (see Fig. 1a). The presence of the ζ-subunit (MW 86 kd) is required to form these polymers, since the core enzyme (α2ββ') does fail to assemble into such structures under these conditions.

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