title: ColE1-Plasmid Production in Escherichia coli: Mathematical Simulation and Experimental Validation.
abstract: Plasmids have become very important as pharmaceutical gene vectors in the fields of gene therapy and genetic vaccination in the past years. In this study, we present a dynamic model to simulate the ColE1-like plasmid replication control, once for a DH5α-strain carrying a low copy plasmid (DH5α-pSUP 201-3) and once for a DH5α-strain carrying a high copy plasmid (DH5α-pCMV-lacZ) by using ordinary differential equations and the MATLAB software. The model includes the plasmid replication control by two regulatory RNA molecules (RNAI and RNAII) as well as the replication control by uncharged tRNA molecules. To validate the model, experimental data like RNAI- and RNAII concentration, plasmid copy number (PCN), and growth rate for three different time points in the exponential phase were determined. Depending on the sampled time point, the measured RNAI- and RNAII concentrations for DH5α-pSUP 201-3 reside between 6 ± 0.7 and 34 ± 7 RNAI molecules per cell and 0.44 ± 0.1 and 3 ± 0.9 RNAII molecules per cell. The determined PCNs averaged between 46 ± 26 and 48 ± 30 plasmids per cell. The experimentally determined data for DH5α-pCMV-lacZ reside between 345 ± 203 and 1086 ± 298 RNAI molecules per cell and 22 ± 2 and 75 ± 10 RNAII molecules per cell with an averaged PCN of 1514 ± 1301 and 5806 ± 4828 depending on the measured time point. As the model was shown to be consistent with the experimentally determined data, measured at three different time points within the growth of the same strain, we performed predictive simulations concerning the effect of uncharged tRNA molecules on the ColE1-like plasmid replication control. The hypothesis is that these tRNA molecules would have an enhancing effect on the plasmid production. The in silico analysis predicts that uncharged tRNA molecules would indeed increase the plasmid DNA production.
authors.affiliation: Abteilung für Proteom- und Metabolomforschung, Fakultät für Biologie, Universität Bielefeld , Bielefeld , Germany.
authors.forename: Inga
authors.initials: I
authors.lastname: Freudenau
authors.affiliation: Abteilung für Proteom- und Metabolomforschung, Fakultät für Biologie, Universität Bielefeld , Bielefeld , Germany.
authors.forename: Petra
authors.initials: P
authors.lastname: Lutter
authors.affiliation: PlasmidFactory GmbH & Co. KG , Bielefeld , Germany.
authors.forename: Ruth
authors.initials: R
authors.lastname: Baier
authors.affiliation: PlasmidFactory GmbH & Co. KG , Bielefeld , Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Schleef
authors.affiliation: Abteilung für Proteom- und Metabolomforschung, Fakultät für Biologie, Universität Bielefeld , Bielefeld , Germany ; Institut für Genomforschung und Systembiologie, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld , Bielefeld , Germany.
authors.forename: Hanna
authors.initials: H
authors.lastname: Bednarz
authors.affiliation: Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana-Cuajimalpa , Mexico City , Mexico.
authors.forename: Alvaro R
authors.initials: AR
authors.lastname: Lara
authors.affiliation: Abteilung für Proteom- und Metabolomforschung, Fakultät für Biologie, Universität Bielefeld , Bielefeld , Germany ; Institut für Genomforschung und Systembiologie, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld , Bielefeld , Germany.
authors.forename: Karsten
authors.initials: K
authors.lastname: Niehaus
keywords: biotechnology; high copy plasmid; modeling; ordinary differential equations; plasmid replication; small RNA; uncharged tRNA