%0 Journal Article %1 ISI:000276821400003 %A Hardiman, Timo %A Meinhold, Hannes %A Hofmann, Johannes %A Ewald, Jennifer C. %A Siemann-Herzberg, Martin %A Reuss, Matthias %C 525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA %D 2010 %I ACADEMIC PRESS INC ELSEVIER SCIENCE %J METABOLIC ENGINEERING %K 1,6-bis(phosphate); Central Cra; Fed-batch; Fructose Gene Glucose-limitation; Growth Position Promoter; RNA Regulation; Transcription carbon fruR; matrix; metabolism; myown network; polymerase; rate-dependent rate} regulation; regulatory volume; weight {Cell %N 3 %P 196-211 %R 10.1016/j.ymben.2009.10.006 %T Prediction of kinetic parameters from DNA-binding site sequences for modeling global transcription dynamics in Escherichia coli %U https://doi.org/10.1016/j.ymben.2009.10.006 %V 12 %X 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.

@article{ISI:000276821400003, abstract = {{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.}}, added-at = {2018-01-25T13:38:08.000+0100}, address = {{525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA}}, affiliation = {{Reuss, M (Reprint Author), Univ Stuttgart, Inst Biochem Engn, Allmandring 31, D-70569 Stuttgart, Germany. Hardiman, Timo; Meinhold, Hannes; Hofmann, Johannes; Ewald, Jennifer C.; Siemann-Herzberg, Martin; Reuss, Matthias, Univ Stuttgart, Inst Biochem Engn, D-70569 Stuttgart, Germany.}}, author = {Hardiman, Timo and Meinhold, Hannes and Hofmann, Johannes and Ewald, Jennifer C. and Siemann-Herzberg, Martin and Reuss, Matthias}, author-email = {{reuss@ibvt.uni-stuttgart.de}}, biburl = {https://puma.ub.uni-stuttgart.de/bibtex/2c7057b127dc37675c33345e07caf8b8f/siemannherzberg}, da = {{2018-01-25}}, doc-delivery-number = {{585JL}}, doi = {{10.1016/j.ymben.2009.10.006}}, eissn = {{1096-7184}}, funding-acknowledgement = {{Baden-Wuerttemberg}}, funding-text = {{The authors would like to thank Andreas Freund, Petra Schlack, Barbara Hormann and Gabriele Vacun for excellent technical assistance; Oliver Vielhauer for competent advice on the enzymatic assay; Karin Lemuth, Tom Schuhmacher and Daniel Pfeiffer for fruitful discussions on mRNA dynamics and related technical questions. We would also like to thank Henning Schmidt and Nikolaus Hansen for providing the software tools used in this study. This work was funded by a grant of the state of Baden-Wuerttemberg within the network research project ``Development of systems biology methods and tools for the analysis of complex cellular networks''.}}, interhash = {1eb1c11521d53baef4eaad339918d351}, intrahash = {c7057b127dc37675c33345e07caf8b8f}, issn = {{1096-7176}}, journal = {{METABOLIC ENGINEERING}}, journal-iso = {{Metab. Eng.}}, keywords = {1,6-bis(phosphate); Central Cra; Fed-batch; Fructose Gene Glucose-limitation; Growth Position Promoter; RNA Regulation; Transcription carbon fruR; matrix; metabolism; myown network; polymerase; rate-dependent rate} regulation; regulatory volume; weight {Cell}, keywords-plus = {{GENETICALLY STRUCTURED MODELS; METABOLIC REACTION NETWORKS; PROMOTER-OPERATOR FUNCTION; GENE-EXPRESSION; GROWTH-RATE; RNA-POLYMERASE; CATABOLITE REPRESSION; SALMONELLA-TYPHIMURIUM; MULTICOPY PLASMIDS; DIAUXIC GROWTH}}, language = {{English}}, month = {{MAY}}, number = {{3}}, number-of-cited-references = {{74}}, pages = {{196-211}}, publisher = {{ACADEMIC PRESS INC ELSEVIER SCIENCE}}, research-areas = {{Biotechnology \& Applied Microbiology}}, researcherid-numbers = {{Wang, Haixin/F-9022-2011}}, times-cited = {{8}}, timestamp = {2018-01-25T12:38:18.000+0100}, title = {{Prediction of kinetic parameters from DNA-binding site sequences for modeling global transcription dynamics in Escherichia coli}}, type = {{Article}}, unique-id = {{ISI:000276821400003}}, url = {https://doi.org/10.1016/j.ymben.2009.10.006}, usage-count-last-180-days = {{0}}, usage-count-since-2013 = {{9}}, volume = {{12}}, web-of-science-categories = {{Biotechnology \& Applied Microbiology}}, year = {{2010}} }