期刊
METABOLIC ENGINEERING
卷 12, 期 3, 页码 196-211出版社
ACADEMIC PRESS INC ELSEVIER SCIENCE
DOI: 10.1016/j.ymben.2009.10.006
关键词
Cell volume; Central carbon metabolism; Cra; Fed-batch; Fructose 1,6-bis(phosphate); fruR; Glucose-limitation; Gene regulatory network; Growth rate-dependent regulation; Position weight matrix; Promoter; Regulation; RNA polymerase; Transcription rate
资金
- Baden-Wuerttemberg
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.
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