scholarly journals The extent of B-form structure in a 6S RNA variant that mimics DNA to bind to the Escherichia coli RNA Polymerase

2018 ◽  
Author(s):  
Nilesh K. Banavali
Keyword(s):  
Escherichia Coli ◽  
Nucleic Acid ◽  
Structural Analysis ◽  
Rna Polymerase ◽  
Rna Structure ◽  
Recent Article ◽  
Single Strand ◽  
Bacterial Rna ◽  
6S Rna

AbstractIn a recent article by Darst and coworkers, it was found that a non-coding 6S RNA variant regulates a bacterial RNA polymerase by mimicking B-Form DNA, and a few different nucleic acid duplex parameters were analyzed to understand the extent of B-form RNA structure. In this manuscript, a different structural analysis based on conformational distance from canonical A-form and B-form single-strand structures is presented. This analysis addresses the occurrence and extent of both local and global B-form structure in the published 6S RNA variant model.

scholarly journals Substitution of a Highly Conserved Histidine in the Escherichia coli Heat Shock Transcription Factor, σ32, Affects Promoter Utilization In Vitro and Leads to Overexpression of the Biofilm-Associated Flu Protein In Vivo

2007 ◽  
Vol 189 (23) ◽  
pp. 8430-8436 ◽  
Author(s):  
Olga V. Kourennaia ◽  
Pieter L. deHaseth
Keyword(s):  
Escherichia Coli ◽  
Heat Shock ◽  
Rna Polymerase ◽  
Sigma Factor ◽  
Stable Complex ◽  
Tryptophan Residue ◽  
Specific Sequence ◽  
Bacterial Rna

ABSTRACT The heat shock sigma factor (σ32 in Escherichia coli) directs the bacterial RNA polymerase to promoters of a specific sequence to form a stable complex, competent to initiate transcription of genes whose products mitigate the effects of exposure of the cell to high temperatures. The histidine at position 107 of σ32 is at the homologous position of a tryptophan residue at position 433 of the main sigma factor of E. coli, σ70. This tryptophan is essential for the strand separation step leading to the formation of the initiation-competent RNA polymerase-promoter complex. The heat shock sigma factors of all gammaproteobacteria sequenced have a histidine at this position, while in the alpha- and deltaproteobacteria, it is a tryptophan. In vitro the alanine-for-histidine substitution at position 107 (H107A) destabilizes complexes between the GroE promoter and RNA polymerase containing σ32, implying that H107 plays a role in formation or maintenance of the strand-separated complex. In vivo, the H107A substitution in σ32 impedes recovery from heat shock (exposure to 42°C), and it also leads to overexpression at lower temperatures (30°C) of the Flu protein, which is associated with biofilm formation.

scholarly journals 6S RNA Mimics B-Form DNA to Regulate Escherichia coli RNA Polymerase

2017 ◽  
Vol 68 (2) ◽  
pp. 388-397.e6 ◽  
Author(s):  
James Chen ◽  
Karen M. Wassarman ◽  
Shili Feng ◽  
Katherine Leon ◽  
Andrey Feklistov ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Rna Polymerase ◽  
6S Rna

6S RNA – an ancient regulator of bacterial RNA polymerase rediscovered

2005 ◽  
Vol 386 (12) ◽  
pp. 1273-1277 ◽  
Author(s):  
Dagmar K. Willkomm ◽  
Roland K. Hartmann
Keyword(s):  
Rna Polymerase ◽  
Dependent Manner ◽  
Bacterial Rna ◽  
Promoter Complex ◽  
6S Rna ◽  
Σ Factor ◽  
Central Bulge ◽  
The Common ◽  
Non Coding Rnas ◽  
Year 2000

AbstractThe bacterial riboregulator 6S RNA was one of the first non-coding RNAs to be discovered in the late 1960s, but its cellular role remained enigmatic until the year 2000. 6S RNA, only recognized to be ubiquitous among bacteria in 2005, binds to RNA polymerase in a σ factor-dependent manner to repress transcription from a subgroup of promoters. The common feature of a double-stranded rod with a central bulge has led to the proposal that 6S RNA may mimic an open promoter complex.

scholarly journals Influence of DNA Template Choice on Transcription and Inhibition of Escherichia coli RNA Polymerase

2012 ◽  
Vol 56 (8) ◽  
pp. 4536-4539 ◽  
Author(s):  
Joerg Haupenthal ◽  
Kristina Hüsecken ◽  
Matthias Negri ◽  
Christine K. Maurer ◽  
Rolf W. Hartmann
Keyword(s):  
Escherichia Coli ◽  
Drug Discovery ◽  
Rna Polymerase ◽  
Sigma Factor ◽  
Inhibitory Potency ◽  
Experimental Conditions ◽  
Early Stages ◽  
Bacterial Rna ◽  
Transcription Efficiency ◽  
Dna Template

ABSTRACTIn recent decades, quantitative transcription assays using bacterial RNA polymerase (RNAP) have been performed under widely diverse experimental conditions. We demonstrate that the template choice can influence the inhibitory potency of RNAP inhibitors. Furthermore, we illustrate that the sigma factor (σ70) surprisingly increases the transcription efficiency of templates with nonphysiological nonprokaryotic promoters. Our results might be a useful guideline in the early stages of using RNAP for drug discovery.

Mapping the Spatial Neighborhood of the Regulatory 6S RNA Bound to Escherichia coli RNA Polymerase Holoenzyme

2013 ◽  
Vol 425 (19) ◽  
pp. 3649-3661 ◽  
Author(s):  
Benedikt Steuten ◽  
Piotr Setny ◽  
Martin Zacharias ◽  
Rolf Wagner
Keyword(s):  
Escherichia Coli ◽  
Rna Polymerase ◽  
6S Rna ◽  
Rna Polymerase Holoenzyme

scholarly journals A T7 phage factor required for managing RpoS inEscherichia coli

2018 ◽  
Author(s):  
Aline Tabib-Salazar ◽  
Bing Liu ◽  
Declan Barker ◽  
Lynn Burchell ◽  
Udi Qimron ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Rna Polymerase ◽  
Stationary Phase ◽  
Stationary Phases ◽  
Specific Inhibitor ◽  
E Coli ◽  
Bacterial Transcription ◽  
Bacterial Rna ◽  
Phage T7 ◽  
T7 Phage

T7 development inEscherichia colirequires the inhibition of the housekeeping form of the bacterial RNA polymerase (RNAP), Eσ70, by two T7 proteins: Gp2 and Gp5.7. While the biological role of Gp2 is well understood, that of Gp5.7 remains to be fully deciphered. Here, we present results from functional and structural analyses to reveal that Gp5.7 primarily serves to inhibit EσS, the predominant form of the RNAP in the stationary phase of growth, which accumulates in exponentially growingE. colias a consequence of buildup of guanosine pentaphosphate ((p)ppGpp) during T7 development. We further demonstrate a requirement of Gp5.7 for T7 development inE. colicells in the stationary phase of growth. Our finding represents a paradigm for how some lytic phages have evolved distinct mechanisms to inhibit the bacterial transcription machinery to facilitate phage development in bacteria in the exponential and stationary phases of growth.Significance statementVirus that infect bacteria (phages) represent the most abundant living entities on the planet and many aspects of our fundamental knowledge of phage-bacteria relationships have been derived in the context of exponentially growing bacteria. In the case of the prototypicalEscherichia coliphage T7, specific inhibition of the housekeeping form of the RNA polymerase (Eσ70) by a T7 protein, called Gp2, is essential for the development of viral progeny. We now reveal that T7 uses a second specific inhibitor that selectively inhibits the stationary phase RNAP (EσS), which enables T7 to develop well in exponentially growing and stationary phase bacteria. The results have broad implications for our understanding of phage-bacteria relationships and therapeutic application of phages.

scholarly journals rRNA Antitermination Functions with Heat Shock Promoters

2003 ◽  
Vol 185 (21) ◽  
pp. 6486-6489 ◽  
Author(s):  
Hyuk Kyu Seoh ◽  
Michelle Weech ◽  
Ning Zhang ◽  
Catherine L. Squires
Keyword(s):  
Escherichia Coli ◽  
Nucleic Acid ◽  
Heat Shock ◽  
Rna Polymerase ◽  
Nucleic Acid Sequence ◽  
Transcription Antitermination

ABSTRACT Transcription antitermination in the rRNA operons of Escherichia coli requires a unique nucleic acid sequence that serves as a signal for modification of the elongating RNA polymerase, making it resistant to Rho-dependent termination. We examined the antitermination ability of RNA polymerase elongation complexes that had initiated at three different heat shock promoters, dnaK, groE, and clpB, and then transcribed the antitermination sequence to read through a Rho-dependent terminator. Terminator bypass comparable to that seen with σ70 promoters was obtained. Lack of or inversion of the sequence abolished terminator readthrough. We conclude that RNA polymerase that uses σ32 to initiate transcription can adopt a conformation similar to that of σ70-containing RNA polymerase, enabling it to interact with auxiliary modifying proteins and bypass Rho-dependent terminators.

scholarly journals Phenotypic consequences of RNA polymerase dysregulation in Escherichia coli

2017 ◽  
Author(s):  
Paramita Sarkar ◽  
Amy Switzer ◽  
Christine Peters ◽  
Joe Pogliano ◽  
Sivaramesh Wigneshweraraj
Keyword(s):  
Escherichia Coli ◽  
Rna Polymerase ◽  
Single Molecule ◽  
Abiotic Factors ◽  
Growth Conditions ◽  
Bacterial Cells ◽  
Adaptive Responses ◽  
Single Molecule Level ◽  
Bacterial Rna ◽  
Transcriptional Rewiring

ABSTRACTMany bacterial adaptive responses to changes in growth conditions due to biotic and abiotic factors involve reprogramming of gene expression at the transcription level. The bacterial RNA polymerase (RNAP), which catalyzes transcription, can thus be considered as the major mediator of cellular adaptive strategies. But how do bacteria respond if a stress factor directly compromises the activity of the RNAP? We used a phage-derived small protein to specifically perturb bacterial RNAP activity in exponentially growing Escherichia coli. Using cytological profiling, tracking RNAP behavior at single-molecule level and transcriptome analysis, we reveal that adaptation to conditions that directly perturb bacterial RNAP performance can result in a biphasic growth behavior and thereby confer the ‘adapted’ bacterial cells an enhanced ability to tolerate diverse antibacterial stresses. The results imply that while synthetic transcriptional rewiring may confer bacteria with the intended desirable properties, such approaches may also collaterally allow them to acquire undesirable traits.

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