Three-dimensional reconstruction of transcription termination factor rho: orientation of the N-terminal domain and visualization of an RNA-binding site

2000 ◽  
Vol 299 (5) ◽  
pp. 1279-1287 ◽  
Author(s):  
Xiong Yu ◽  
Taigo Horiguchi ◽  
Katsuya Shigesada ◽  
Edward H. Egelman
Keyword(s):  
Binding Site ◽  
Rna Binding ◽  
Transcription Termination ◽  
Three Dimensional ◽  
Three Dimensional Reconstruction ◽  
Termination Factor ◽  
Terminal Domain ◽  
Transcription Termination Factor ◽  
Dimensional Reconstruction

scholarly journals Effects of Bicyclomycin on RNA- and ATP-Binding Activities of Transcription Termination Factor Rho

1998 ◽  
Vol 42 (3) ◽  
pp. 571-578 ◽  
Author(s):  
Lucia Carrano ◽  
Cecilia Bucci ◽  
Roberto De Pascalis ◽  
Alfredo Lavitola ◽  
Filomena Manna ◽  
...  
Keyword(s):  
Rna Binding ◽  
Transcription Termination ◽  
Gel Filtration ◽  
Experimental System ◽  
Cross Linking ◽  
Atp Binding ◽  
Mobility Shift ◽  
Termination Factor ◽  
Transcription Termination Factor

ABSTRACT Bicyclomycin is a commercially important antibiotic that has been shown to be effective against many gram-negative bacteria. Genetic and biochemical evidence indicates that the antibiotic interferes with RNA metabolism in Escherichia coli by inhibiting the activity of transcription termination factor Rho. However, the precise mechanism of inhibition is not completely known. In this study we have used in vitro transcription assays to analyze the effects of bicyclomycin on the termination step of transcription. The Rho-dependent transcription termination region located within thehisG cistron of Salmonella typhimurium has been used as an experimental system. The possible interference of the antibiotic with the various functions of factor Rho, such as RNA binding at the primary site, ATP binding, and hexamer formation, has been investigated by RNA gel mobility shift, photochemical cross-linking, and gel filtration experiments. The results of these studies demonstrate that bicyclomycin does not interfere with the binding of Rho to the loading site on nascent RNA. Binding of the factor to ATP is not impeded, on the contrary, the antibiotic appears to decrease the apparent equilibrium dissociation constant for ATP in photochemical cross-linking experiments. The available evidence suggests that this decrease might be due to an interference with the correct positioning of ATP within the nucleotide-binding pocket leading b an inherent block of ATP hydrolysis. Possibly, as a consequence of this interference, the antibiotic also prevents ATP-dependent stabilization of Rho hexamers.

Crystal structure of the RNA-binding domain from transcription termination factor rho

1998 ◽  
Vol 5 (5) ◽  
pp. 352-356 ◽  
Author(s):  
Timothy J. Allison ◽  
Todd C. Wood ◽  
Deborah M. Briercheck ◽  
Fraydoon Rastinejad ◽  
John P. Richardson ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Rna Binding ◽  
Transcription Termination ◽  
Binding Domain ◽  
Termination Factor ◽  
Transcription Termination Factor ◽  
Rna Binding Domain

Methods for three-dimensional reconstruction of cellular components within a thick section

1986 ◽  
Vol 44 ◽  
pp. 18-21
Author(s):  
J. Frank ◽  
B. F. McEwen ◽  
M. Radermacher ◽  
C. L. Rieder
Keyword(s):  
Tilt Angle ◽  
Tomographic Reconstruction ◽  
3D Structure ◽  
Three Dimensional ◽  
Thick Section ◽  
Three Dimensional Reconstruction ◽  
Axis Ratio ◽  
Dimensional Reconstruction ◽  
Cellular Components

The tomographic reconstruction from multiple projections of cellular components, within a thick section, offers a way of visualizing and quantifying their three-dimensional (3D) structure. However, asymmetric objects require as many views from the widest tilt range as possible; otherwise the reconstruction may be uninterpretable. Even if not for geometric obstructions, the increasing pathway of electrons, as the tilt angle is increased, poses the ultimate upper limitation to the projection range. With the maximum tilt angle being fixed, the only way to improve the faithfulness of the reconstruction is by changing the mode of the tilting from single-axis to conical; a point within the object projected with a tilt angle of 60° and a full 360° azimuthal range is then reconstructed as a slightly elliptic (axis ratio 1.2 : 1) sphere.

Three-Dimensional Reconstruction of Native Androctonus Australis Hemocyanin

1990 ◽  
Vol 48 (1) ◽  
pp. 452-453
Author(s):  
Nicolas Boisset ◽  
Jean-Christophe Taveau ◽  
Jean Lamy ◽  
Terence Wagenknecht ◽  
Michael Radermacher ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Solid Body ◽  
Body Surface ◽  
Three Dimensional ◽  
Staining Technique ◽  
Three Dimensional Reconstruction ◽  
Dimensional Reconstruction ◽  
View Reconstruction ◽  
Surface Representations ◽  
Top View

Hemocyanin, the respiratory pigment of the scorpion Androctonus australis is composed of 24 kidney shaped subunits. A model of architecture supported by many indirect arguments has been deduced from electron microscopy (EM) and immuno-EM. To ascertain, the disposition of the subunits within the oligomer, the 24mer was submitted to three-dimensional reconstruction by the method of single-exposure random-conical tilt series.A sample of native hemocyanin, prepared with the double layer negative staining technique, was observed by transmisson electron microscopy under low-dose conditions. Six 3D-reconstructions were carried out indenpendently from top, side and 45°views. The results are composed of solid-body surface representations, and slices extracted from the reconstruction volume.The main two characters of the molecule previously reported by Van Heel and Frank, were constantly found in the solid-body surface representations. These features are the presence of two different faces called flip and flop and a rocking of the molecule around an axis passing through diagonnally opposed hexamers. Furthermore, in the solid-body surface of the top view reconstruction, the positions and orientations of the bridges connecting the half molecules were found in excellent agreement with those predicted by the model.

Three-Dimensional Reconstruction of Two Forms of the Chaperonin GRO EL

1990 ◽  
Vol 48 (1) ◽  
pp. 258-259
Author(s):  
J.L. Carrascosa ◽  
G. Abella ◽  
S. Marco ◽  
M. Muyal ◽  
J.M. Carazo
Keyword(s):  
Three Dimensional ◽  
The Other ◽  
Two Dimensional ◽  
Series Method ◽  
Three Dimensional Reconstruction ◽  
Structural Components ◽  
E Coli ◽  
Dimensional Reconstruction ◽  
Morphogenetic Factors ◽  
Tilt Series

Chaperonins are a class of proteins characterized by their role as morphogenetic factors. They trantsiently interact with the structural components of certain biological aggregates (viruses, enzymes etc), promoting their correct folding, assembly and, eventually transport. The groEL factor from E. coli is a conspicuous member of the chaperonins, as it promotes the assembly and morphogenesis of bacterial oligomers and/viral structures.We have studied groEL-like factors from two different bacteria:E. coli and B.subtilis. These factors share common morphological features , showing two different views: one is 6-fold, while the other shows 7 morphological units. There is also a correlation between the presence of a dominant 6-fold view and the fact of both bacteria been grown at low temperature (32°C), while the 7-fold is the main view at higher temperatures (42°C). As the two-dimensional projections of groEL were difficult to interprete, we studied their three-dimensional reconstruction by the random conical tilt series method from negatively stained particles.

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