A thermodynamic model of bacterial transcription

Transcriptional pausing is highly regulated by the template DNA and nascent transcript sequences. Here, we propose a thermodynamic model of transcriptional pausing, based on the thermal energy of transcription bubbles and nascent RNA structures, to describe the kinetics of the reaction pathways between active translocation, intermediate, backtracked, and hairpin-stabilized pauses. The model readily predicts experimentally detected pauses in high-resolution optical tweezers measurements of transcription. Unlike other models, it also predicts the effect of tension and the GreA transcription factor on pausing.

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Kinetic Analysis of tRNA-Directed Transcription Antitermination of the Bacillus subtilis glyQS Gene In Vitro

Journal of Bacteriology ◽

10.1128/jb.186.16.5392-5399.2004 ◽

2004 ◽

Vol 186 (16) ◽

pp. 5392-5399 ◽

Cited By ~ 38

Author(s):

Frank J. Grundy ◽

Tina M. Henkin

Keyword(s):

Bacillus Subtilis ◽

Assay System ◽

Nascent Transcript ◽

Vitro Assay ◽

T Box ◽

Transcription Antitermination ◽

Transcriptional Pausing ◽

Transcription Complexes ◽

Kinetics Of

ABSTRACT Binding of uncharged tRNA to the nascent transcript promotes readthrough of a leader region transcription termination signal in genes regulated by the T box transcription antitermination mechanism. Each gene in the T box family responds independently to its cognate tRNA, with specificity determined by base pairing of the tRNA to the leader at the anticodon and acceptor ends of the tRNA. tRNA binding stabilizes an antiterminator element in the transcript that sequesters sequences that participate in formation of the terminator helix. tRNAGly-dependent antitermination of the Bacillus subtilis glyQS leader was previously demonstrated in a purified in vitro assay system. This assay system was used to investigate the kinetics of transcription through the glyQS leader and the effect of tRNA and transcription elongation factors NusA and NusG on transcriptional pausing and antitermination. Several pause sites, including a major site in the loop of stem III of the leader, were identified, and the effect of modulation of pausing on antitermination efficiency was analyzed. We found that addition of tRNAGly can promote antitermination as long as the tRNA is added before the majority of the transcription complexes reach the termination site, and variations in pausing affect the requirements for timing of tRNA addition.

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Kinetics of Substituted Bis- and Mono-azo Dyes as Corrosion Inhibitors for Aluminium in Hydrochloric Acid and Sodium Hydroxide Solutions

Journal of Chemical Research ◽

10.1177/174751989902300702 ◽

1999 ◽

Vol 23 (7) ◽

pp. 408-409

Author(s):

Loutfy H. Madkour ◽

R. M. Issa ◽

I. M. El-Ghrabawy

Keyword(s):

Hydrochloric Acid ◽

Sodium Hydroxide ◽

Azo Dyes ◽

Thermodynamic Model ◽

Corrosion Inhibitors ◽

Kinetics Of ◽

Alkaline Corrosion

This investigation is designed to apply an advanced kinetic–thermodynamic model on the data obtained from acidic and alkaline corrosion of aluminium using bis- and mono-azo dyes as corrosion inhibitors.

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Kinetics of lipopolysaccharide-induced transcription factor activation/inactivation and relation to proinflammatory gene expression in the murine spleen

Toxicology and Applied Pharmacology ◽

10.1016/s0041-008x(02)00077-7 ◽

2003 ◽

Vol 187 (3) ◽

pp. 147-161 ◽

Cited By ~ 27

Author(s):

Hui-Ren Zhou ◽

Zahidul Islam ◽

James J Pestka

Keyword(s):

Gene Expression ◽

Transcription Factor ◽

Transcription Factor Activation ◽

Murine Spleen ◽

Proinflammatory Gene ◽

Kinetics Of ◽

Proinflammatory Gene Expression

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Minor Alterations in Core Promoter Element Positioning Reveal Functional Plasticity of a Bacterial Transcription Factor

mBio ◽

10.1128/mbio.02753-21 ◽

2021 ◽

Author(s):

Wamiah P. Chowdhury ◽

Kenneth A. Satyshur ◽

James L. Keck ◽

Patricia J. Kiley

Keyword(s):

Transcription Factor ◽

Core Promoter ◽

Promoter Element ◽

Functional Plasticity ◽

Iron Sulfur Cluster ◽

Content Type ◽

E Coli ◽

Bacterial Transcription ◽

Iron Sulfur ◽

Living Organisms

Transcription regulation is a key process in all living organisms, involving a myriad of transcription factors. In E. coli , the regulator of the iron-sulfur cluster biogenesis pathway, IscR, acts as a global transcription factor, activating the transcription of some pathways and repressing others.

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Nerve growth factor induces the expression of the LIM homeodomain transcription factor Isl-1 with the kinetics of an immediate early gene in adult rat dorsal root ganglion

Neuroscience Letters ◽

10.1016/s0304-3940(01)02040-7 ◽

2001 ◽

Vol 309 (2) ◽

pp. 130-134 ◽

Cited By ~ 1

Author(s):

H.L. Jameson ◽

K.A. Lillycrop

Keyword(s):

Transcription Factor ◽

Nerve Growth Factor ◽

Growth Factor ◽

Dorsal Root Ganglion ◽

Dorsal Root ◽

Early Gene ◽

Immediate Early ◽

Homeodomain Transcription Factor ◽

Adult Rat ◽

Kinetics Of

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Dynamic epistasis analysis reveals how chromatin remodeling regulates transcriptional bursting

10.1101/2021.12.15.472793 ◽

2021 ◽

Author(s):

Ineke Brouwer ◽

Emma Kerklingh ◽

Fred van Leeuwen ◽

Tineke L Lenstra

Keyword(s):

Transcription Factor ◽

Chromatin Remodeling ◽

Single Molecule ◽

Binding Sites ◽

Live Cell Imaging ◽

Cell Imaging ◽

Nucleosome Remodeling ◽

Epistasis Analysis ◽

Transcriptional Bursting ◽

Kinetics Of

Transcriptional bursting has been linked to the stochastic positioning of nucleosomes. However, how bursting is regulated by remodeling of promoter nucleosomes is unknown. Here, we use single-molecule live-cell imaging of GAL10 transcription in budding yeast to measure how transcriptional bursting changes upon single and double perturbations of chromatin remodeling factors, the transcription factor Gal4 and preinitiation complex (PIC) components. Using dynamic epistasis analysis, we reveal how remodeling of different nucleosomes regulates individual transcriptional bursting parameters. At the nucleosome covering the Gal4 binding sites, RSC acts synergistically with Gal4 binding to facilitate each burst. Conversely, nucleosome remodeling at the TATA box controls only the first burst upon galactose induction. In the absence of remodelers, nucleosomes at canonical TATA boxes are displaced by TBP binding to allow for transcription activation. Overall, our results reveal how promoter nucleosome remodeling, together with transcription factor and PIC binding regulates the kinetics of transcriptional bursting.

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Combustion Characteristics of Hydrochar and Pyrochar Derived from Digested Sewage Sludge

Energies ◽

10.3390/en13164164 ◽

2020 ◽

Vol 13 (16) ◽

pp. 4164 ◽

Cited By ~ 1

Author(s):

Pablo J. Arauzo ◽

María Atienza-Martínez ◽

Javier Ábrego ◽

Maciej P. Olszewski ◽

Zebin Cao ◽

...

Keyword(s):

Sewage Sludge ◽

Reaction Pathways ◽

Energy Yield ◽

Combustion Kinetics ◽

Coal Blending ◽

Carbon Recovery ◽

And Storage ◽

Kinetics Of ◽

Digested Sewage Sludge ◽

Lower Carbon

In this paper, hydrochars and pyrochars were produced at 260 °C under different residence times (2 and 4 h) using anaerobic digested sewage sludge (SSL) as initial feedstock. The effect of reaction time on the fuel properties of hydrochars and pyrochars was evaluated. Moreover, the combustion kinetics of raw SSL and the derived pyrochars and hydrochars without coal blending were determined at two different air flows (20 and 90 mL/min) and compared. In the same conditions, the yield of hydrochar was significantly lower than that of pyrochar, confirming the different reaction pathways followed in each process. The results showed hydrochars have lower carbon recovery and energy yield than pyrochars, making the latter more suitable for energy purposes. The thermogravimetric combustion study showed that both thermochemical treatments increased the ignition temperature but decreased the burnout temperature, which results in higher stability during handling and storage. However, raw SSL is better for combustion than hydrochar according to the combustibility index. In addition, the kinetic study showed that the activation energy of the combustion of biochars, especially pyrochar, is lower than that of raw SSL, which is advantageous for their combustion.

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