PUMA publications for /tag/volume;%201,6-bis(phosphate);%20matrix;%20cra;%20gene%20carbonhttps://puma.ub.uni-stuttgart.de/tag/volume;%201,6-bis(phosphate);%20matrix;%20cra;%20gene%20carbonPUMA RSS feed for /tag/volume;%201,6-bis(phosphate);%20matrix;%20cra;%20gene%20carbon2024-03-30T00:11:25+01:00Prediction of kinetic parameters from DNA-binding site sequences for
modeling global transcription dynamics in Escherichia colihttps://puma.ub.uni-stuttgart.de/bibtex/2c7057b127dc37675c33345e07caf8b8f/siemannherzbergsiemannherzberg2018-01-25T13:38:08+01:00myown Fed-batch; Position weight Promoter; Cra; rate} regulation; Glucose-limitation; metabolism; Fructose 1,6-bis(phosphate); matrix; polymerase; rate-dependent fruR; Growth RNA network; Transcription regulatory Central volume; Gene carbon Regulation; {Cell <span data-person-type="author" class="authorEditorList "><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Timo Hardiman" itemprop="url" href="/person/11eb1c11521d53baef4eaad339918d351/author/0"><span itemprop="name">T. Hardiman</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Hannes Meinhold" itemprop="url" href="/person/11eb1c11521d53baef4eaad339918d351/author/1"><span itemprop="name">H. Meinhold</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Johannes Hofmann" itemprop="url" href="/person/11eb1c11521d53baef4eaad339918d351/author/2"><span itemprop="name">J. Hofmann</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Jennifer C. Ewald" itemprop="url" href="/person/11eb1c11521d53baef4eaad339918d351/author/3"><span itemprop="name">J. Ewald</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Martin Siemann-Herzberg" itemprop="url" href="/person/11eb1c11521d53baef4eaad339918d351/author/4"><span itemprop="name">M. Siemann-Herzberg</span></a></span>, </span> and <span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Matthias Reuss" itemprop="url" href="/person/11eb1c11521d53baef4eaad339918d351/author/5"><span itemprop="name">M. Reuss</span></a></span></span>. </span><span class="additional-entrytype-information"><span itemtype="http://schema.org/PublicationIssue" itemscope="itemscope" itemprop="isPartOf"><em><span itemprop="journal">METABOLIC ENGINEERING</span>, </em> <em><span itemtype="http://schema.org/PublicationVolume" itemscope="itemscope" itemprop="isPartOf"><span itemprop="volumeNumber">12 </span></span>(<span itemprop="issueNumber">3</span>):
<span itemprop="pagination">196-211</span></em> </span>(<em><span>May 2010<meta content="May 2010" itemprop="datePublished"/></span></em>)</span>Thu Jan 25 13:38:08 CET 2018{525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA}{METABOLIC ENGINEERING}{MAY}{3}{196-211}{Prediction of kinetic parameters from DNA-binding site sequences for
modeling global transcription dynamics in Escherichia coli}{Article}{12}{2010}myown Fed-batch; Position weight Promoter; Cra; rate} regulation; Glucose-limitation; metabolism; Fructose 1,6-bis(phosphate); matrix; polymerase; rate-dependent fruR; Growth RNA network; Transcription regulatory Central volume; Gene carbon Regulation; {Cell {The majority of dynamic gene regulatory network (GRN) models are
comprised of only a few genes and do not take multiple transcription
regulation into account. The models are conceived in this way in order
to minimize the number of kinetic parameters. In this paper, we propose
a new approach for predicting kinetic parameters from DNA-binding site
sequences by correlating the protein-DNA binding affinities with
nucleotide sequence conservation. We present the dynamic modeling of the
cra modulon transcription in Escherichia coli during glucose-limited
fed-batch cultivation. The concentration of the Cra regulator protein
inhibitor, fructose1,6-bis(phosphate), decreases sharply, eventually
leading to the repression of transcription. Total RNA concentration data
indicate a strong regulation of transcription through the availability
of RNA polymerase. A critical assessment of the results of the model
simulations supports this finding. This new approach for the prediction
of transcription dynamics may improve the metabolic engineering of gene
regulation processes. (C) 2009 Published by Elsevier Inc.}