Promoter islandsas a platform for interaction with nucleoid proteins and transcription factors

2014 ◽  
Vol 12 (02) ◽  
pp. 1441006 ◽  
Author(s):  
Yuri A. Purtov ◽  
Olga A. Glazunova ◽  
Sergey S. Antipov ◽  
Viktoria O. Pokusaeva ◽  
Eugeny E. Fesenko ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Transcription Factors ◽  
Rna Polymerase ◽  
Binding Sites ◽  
Inhibitory Effect ◽  
Computer Search ◽  
Biologically Relevant ◽  
Bacterial Nucleoid ◽  
Foreign Genes ◽  
Transcriptional Output

Seventy-eight promoter islands with an extraordinarily high density of potential promoters have been recently found in the genome of Escherichia coli. It has been shown that RNA polymerase binds internal promoters of these islands and produces short oligonucleotides, while the synthesis of normal mRNAs is suppressed. This quenching may be biologically relevant, as most islands are associated with foreign genes, which expression may deplete cellular resources. However, a molecular mechanism of silencing with the participation of these promoter-rich regions remains obscure. It has been demonstrated that all islands interact with histone-like protein H-NS — a specific sentinel of foreign genes. In this study, we demonstrated the inhibitory effect of H-NS using Δhns mutant of Escherichia coli and showed that deletion of dps, encoding another protein of bacterial nucleoid, tended to decrease rather than increase the amount of island-specific transcripts. This observation precluded consideration of promoter islands as sites for targeted heterochromatization only and a computer search for the binding sites of 53 transcription factors (TFs) revealed six proteins, which may specifically regulate their transcriptional output.

Characterization of monoclonal antibodies against Escherichia coli core RNA polymerase

2002 ◽  
Vol 361 (2) ◽  
pp. 347-354 ◽  
Author(s):  
Jöelle ROUBY ◽  
Martine PUGNIERE ◽  
Jean-Claude MANI ◽  
Claude GRANIER ◽  
Pierrette MONMOUTON ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Monoclonal Antibodies ◽  
Transcription Factors ◽  
Rna Polymerase ◽  
Binding Sites ◽  
Β Subunit ◽  
Allosteric Interaction ◽  
C Terminus ◽  
Multiple Interactions

Multiple interactions with DNA, RNA and transcription factors occur in a transcription cycle. To survey the proximity of some of these factors to the Escherichiacoli RNA polymerase surface, we produced a set of nine monoclonal antibodies (mAbs) against the enzyme. These mAbs, located at different places on the surface of the enzyme, were used in a co-immunopurification assay to investigate interference with the binding of NusA, σ70, GreB and HepA to core RNA polymerase. One of these mAbs turned out to be the first antibody inhibitor of the binding of NusA and σ70; it did not affect GreB and HepA interactions. Its epitope was located on the β′ subunit at the C-terminus of region G. The properties of this mAb reinforce the idea that the mutually exclusive binding of NusA and σ70 to core RNA polymerase is due to, at least partially, overlapping binding sites, rather than allosteric interaction between two distant binding sites. This mAb is also useful to understand the occupancy of σ70, NusA and Gre proteins on core RNA polymerase.

scholarly journals Structure-function comparisons of (p)ppApp vs (p)ppGpp for Escherichia coli RNA polymerase binding sites and for rrnB P1 promoter regulatory responses in vitro

2018 ◽  
Vol 1861 (8) ◽  
pp. 731-742 ◽  
Author(s):  
Bożena Bruhn-Olszewska ◽  
Vadim Molodtsov ◽  
Michał Sobala ◽  
Maciej Dylewski ◽  
Katsuhiko S. Murakami ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Rna Polymerase ◽  
Structure Function ◽  
Binding Sites ◽  
Polymerase Binding

scholarly journals Evolutionarily conserved transcription factors drive the oxidative stress response in Drosophila

2020 ◽  
Vol 223 (14) ◽  
pp. jeb221622
Author(s):  
Sarah M. Ryan ◽  
Kaitie Wildman ◽  
Briseida Oceguera-Perez ◽  
Scott Barbee ◽  
Nathan T. Mortimer ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Stress Responses ◽  
Binding Sites ◽  
Regulatory Elements ◽  
Genomic Locus ◽  
Biologically Relevant ◽  
Protein Levels ◽  
Putative Transcription Factor

ABSTRACTAs organisms are constantly exposed to the damaging effects of oxidative stress through both environmental exposure and internal metabolic processes, they have evolved a variety of mechanisms to cope with this stress. One such mechanism is the highly conserved p38 MAPK (p38K) pathway, which is known to be post-translationally activated in response to oxidative stress, resulting in the activation of downstream antioxidant targets. However, little is known about the role of p38K transcriptional regulation in response to oxidative stress. Therefore, we analyzed the p38K gene family across the genus Drosophila to identify conserved regulatory elements. We found that oxidative stress exposure results in increased p38K protein levels in multiple Drosophila species and is associated with increased oxidative stress resistance. We also found that the p38Kb genomic locus includes conserved AP-1 and lola-PT transcription factor consensus binding sites. Accordingly, over-expression of these transcription factors in D. melanogaster is sufficient to induce transcription of p38Kb and enhances resistance to oxidative stress. We further found that the presence of a putative lola-PT binding site in the p38Kb locus of a given species is predictive of the species' survival in response to oxidative stress. Through our comparative genomics approach, we have identified biologically relevant putative transcription factor binding sites that regulate the expression of p38Kb and are associated with resistance to oxidative stress. These findings reveal a novel mode of regulation for p38K genes and suggest that transcription may play as important a role in p38K-mediated stress responses as post-translational modifications.

scholarly journals DIFFERENTIAL INHIBITORY EFFECTS OF CHOLERA TOXOIDS AND GANGLIOSIDE ON THE ENTEROTOXINS OF VIBRIO CHOLERAE AND ESCHERICHIA COLI

1973 ◽  
Vol 137 (4) ◽  
pp. 1009-1023 ◽  
Author(s):  
Nathaniel F. Pierce
Keyword(s):  
Escherichia Coli ◽  
Binding Sites ◽  
Competitive Inhibitor ◽  
Inhibitory Effect ◽  
Inhibitory Effects ◽  
E Coli ◽  
Stable Component ◽  
Heat Stable ◽  
Cholera Enterotoxin ◽  
Gut Mucosa

Natural cholera toxoid appears to act as a competitive inhibitor of cholera enterotoxin and is thus a useful tool for studying the interaction of cholera enterotoxin with cell membranes. Cholera enterotoxin binds to gut mucosa more rapidly than does its natural toxoid. Once binding occurs, however, it appears to be prolonged for both materials. Formalinized cholera toxoid has no inhibitory effect upon cholera enterotoxin. Enterotoxic activity, ability to bind to gut mucosa, and antitoxigenicity appear to be independent properties of cholera enterotoxin. Natural cholera toxoid does not inhibit Escherichia coli enterotoxin, indicating that although the two enterotoxins activate the same mucosal secretory mechanism they occupy different binding sites in the mucosa. Ganglioside, which may be the mucosal receptor of cholera enterotoxin, is highly efficient in deactivating cholera enterotoxin. By contrast, ganglioside is relatively inefficient in deactivating heat-labile E. coli enterotoxin and is without effect upon the heat-stable component of E. coli enterotoxin. These findings suggest that ganglioside is not likely to be the mucosal receptor for E. coli enterotoxin. Differences in cellular binding of E. coli and cholera enterotoxins may explain, at least in part, the marked differences in the time of onset and duration of their effects upon gut secretion.

scholarly journals Escherichia coli DksA Binds to Free RNA Polymerase with Higher Affinity than to RNA Polymerase in an Open Complex

2009 ◽  
Vol 191 (18) ◽  
pp. 5854-5858 ◽  
Author(s):  
Christopher W. Lennon ◽  
Tamas Gaal ◽  
Wilma Ross ◽  
Richard L. Gourse
Keyword(s):  
Escherichia Coli ◽  
Transcription Factor ◽  
Rna Polymerase ◽  
Binding Affinity ◽  
Quantitative Assay ◽  
Secondary Channel ◽  
Apparent Affinity ◽  
Transcriptional Output

ABSTRACT The transcription factor DksA binds in the secondary channel of RNA polymerase (RNAP) and alters transcriptional output without interacting with DNA. Here we present a quantitative assay for measuring DksA binding affinity and illustrate its utility by determining the relative affinities of DksA for three different forms of RNAP. Whereas the apparent affinities of DksA for RNAP core and holoenzyme are the same, the apparent affinity of DksA for RNAP decreases almost 10-fold in an open complex. These results suggest that the conformation of RNAP present in an open complex is not optimal for DksA binding and that DNA directly or indirectly alters the interface between the two proteins.

Synthesis of the uracil analog of thuringiensin and its inhibitory effect on DNA-dependent RNA polymerase of Escherichia coli

1981 ◽  
Vol 46 (3) ◽  
pp. 667-672 ◽  
Author(s):  
Ladislav Kalvoda ◽  
Květa Horská ◽  
Karel Šebesta
Keyword(s):  
Escherichia Coli ◽  
Rna Polymerase ◽  
Inhibitory Effect ◽  
Parent Substance ◽  
Inhibition Constant ◽  
Natural Substrate

An analog of thuringiensin (II), containing uracil instead of adenine, was synthetized by the method employed for thuringiensin. Similarly to the parent substance this analog inhibits the DNA-dependent RNA polymerase of Escherichia coli, simultaneously competing with the natural substrate, i.e. UTP. The inhibition constant (Ki = 30 μm) shows that the uracil analog of thuringiensin is an inhibitor of RNA polymerase roughly as efficient as thuringiensin.

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