title: Simplified mechanistic models of gene regulation for analysis and design.
abstract: Simplified mechanistic models of gene regulation are fundamental to systems biology and essential for synthetic biology. However, conventional simplified models typically have outputs that are not directly measurable and are based on assumptions that do not often hold under experimental conditions. To resolve these issues, we propose a 'model reduction' methodology and simplified kinetic models of total mRNA and total protein concentration, which link measurements, models and biochemical mechanisms. The proposed approach is based on assumptions that hold generally and include typical cases in systems and synthetic biology where conventional models do not hold. We use novel assumptions regarding the 'speed of reactions', which are required for the methodology to be consistent with experimental data. We also apply the methodology to propose simplified models of gene regulation in the presence of multiple protein binding sites, providing both biological insights and an illustration of the generality of the methodology. Lastly, we show that modelling total protein concentration allows us to address key questions on gene regulation, such as efficiency, burden, competition and modularity.
authors.affiliation: Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, UK.
authors.forename: Edward J
authors.initials: EJ
authors.lastname: Hancock
authors.affiliation: Department of Bioengineering & Centre for Synthetic Biology and Innovation, Imperial College London, London SW7 2AZ, UK g.stan@imperial.ac.uk.
authors.forename: Guy-Bart
authors.initials: GB
authors.lastname: Stan
authors.affiliation: Department of Bioengineering & Centre for Synthetic Biology and Innovation, Imperial College London, London SW7 2AZ, UK.
authors.forename: James A J
authors.initials: JA
authors.lastname: Arpino
authors.affiliation: Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, UK.
authors.forename: Antonis
authors.initials: A
authors.lastname: Papachristodoulou
mesh_terms: D005786:Gene Expression Regulation / Q000502:physiology*; D008954:Models, Biological; D014176:Protein Biosynthesis / Q000502:physiology*; D012333:RNA, Messenger / Q000096:biosynthesis*
chemical_list: D012333:RNA, Messenger
keywords: gene regulatory networks; mechanistic models; reduced models; synthetic biology; systems biology