Basic Regulatory Principles of Escherichia coli ’ Electron Transport Chain for Varying Oxygen Conditions Sebastian G. Henkel 1¤ , Alexander Ter Beek 2 , Sonja Steinsiek 3 , Stefan Stagge 3 , Katja Bettenbrock 3 , M. Joost Teixeira de Mattos 2 , Thomas Sauter 4 , Oliver Sawodny 1 , Michael Ederer 1 * 1 Institute for System Dynamics, University of Stuttgart, Stuttgart, Germany, 2 Molecular Microbial Physiology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands, 3 Experimental Systems Biology, Max-Planck-Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany, 4 Life Science Research Unit, Universite ´ du Luxembourg, Luxembourg, Luxembourg Abstract For adaptation between anaerobic, micro-aerobic and aerobic conditions Escherichia coli’s metabolism and in particular its electron transport chain (ETC) is highly regulated. Although it is known that the global transcriptional regulators FNR and ArcA are involved in oxygen response it is unclear how they interplay in the regulation of ETC enzymes under micro-aerobic chemostat conditions. Also, there are diverse results which and how quinones (oxidised/reduced, ubiquinone/other quinones) are controlling the ArcBA two-component system. In the following a mathematical model of the E. coli ETC linked to basic modules for substrate uptake, fermentation product excretion and biomass formation is introduced. The kinetic modelling focusses on regulatory principles of the ETC for varying oxygen conditions in glucose-limited continuous cultures. The model is based on the balance of electron donation (glucose) and acceptance (oxygen or other acceptors). Also, it is able to account for different chemostat conditions due to changed substrate concentrations and dilution rates. The parameter identification process is divided into an estimation and a validation step based on previously published and new experimental data. The model shows that experimentally observed, qualitatively different behaviour of the ubiquinone redox state and the ArcA activity profile in the micro-aerobic range for different experimental conditions can emerge from a single network structure. The network structure features a strong feed-forward effect from the FNR regulatory system to the ArcBA regulatory system via a common control of the dehydrogenases of the ETC. The model supports the hypothesis that ubiquinone but not ubiquinol plays a key role in determining the activity of ArcBA in a glucose-limited chemostat at micro-aerobic conditions. Citation: Henkel SG, Ter Beek A, Steinsiek S, Stagge S, Bettenbrock K, et al. (2014) Basic Regulatory Principles of Escherichia coli ’s Electron Transport Chain for Varying Oxygen Conditions. PLoS ONE 9(9): e107640. doi:10.1371/journal.pone.0107640 Editor: Ne ´stor V. Torres, Universidad de La Laguna, Spain Received March 21, 2014; Accepted August 11, 2014; Published September 30, 2014 Copyright: ß 2014 Henkel et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability: The authors confirm that all data underlying the findings are fully available without restriction. All relevant data are within the Supporting Information files. Funding: This work was supported and funded by the German Federal Ministry of Education and Research (BMBF) and the Netherlands Organisation for Scientific Research (NWO) within the SysMO initiative Systems Biology of Microorganisms, (www.sysmo.net). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * Email: michael.ederer@isys.uni-stuttgart.de ¤ Current address: BioControl Jena GmbH, Jena, Germany Introduction Microbial cells are able to adapt to different environmental conditions like temperature, pH, water activity, oxygen availability or substrate type. This requires reorganisation of the metabolism in order to reach short and long term adaptations. A quantitative and systems-level understanding of these processes will expand our insight of regulatory principles and can contribute to the elucidation of molecular mechanisms. Further, this knowledge can be employed in applied industrial settings, e.g. optimised production of organic compounds. Escherichia coli is a facultative anaerobic microorganism, i.e. it can survive at various levels of oxygenation, [1,2]. Those levels can be assigned to fully anaerobic, fully aerobic and intermediate micro-aerobic conditions. In the complete absence of oxygen (0% aerobiosis, anaerobiosis) or any other external electron acceptor the cell’s fermentative pathways are active. Increased oxygen availability leads to the micro-aerobic (semi-aerobic) state which is an intermediate range where both fermentative and respiratory pathways are active. If the oxygen availability increases above a certain threshold no more fermentation products are excreted. Thus, full aerobiosis (100% aerobiosis) can be defined for the minimal oxygen inflow without any net production of fermenta- tion products like acetate. As reported earlier, in glucose limited continuous cultures of E. coli the respective steady state acetate fluxes show a linear decrease to zero from 0% to 100% aerobiosis, [3–6]. This definition of the aerobiosis scale offers the possibility to get comparable measurement data across different experimental settings and laboratories. A limitation of this definition is that fully aerobic E. coli populations produce acetate at certain experimen- tal conditions. This overflow metabolism occurs for high growth rates in the wild-type [7] and for some mutants (e.g. DsdhC) already at lower growth rates [8]. Therefore, the aerobiosis scale can be applied to micro-aerobic steady state experiments of glucose-limited continuous cultures of wild-type E. coli at low dilution rates. PLOS ONE | www.plosone.org 1 September 2014 | Volume 9 | Issue 9 | e107640 s