Analytical approach for the calculation of promoter activities based on fluorescent protein expression data

Abstract

Characterisation of promoters, repressors, enhancers and so on, is not only essential for unravelling the inner workings of gene regulation, but also to enable the rational engineering of novel synthetic elements. Each putative regulatory region requires experimental assessment across a range of chassis and growth conditions, in order to be categorised as a fully defined functional element. In most studies, promoter activity is represented as the magnitude of a reporter signal, usually fluorescence, normalised to the biomass, as given by the optical density (OD). Such experimental values are often obtained from a coupled time-series experiment. Applying simple mathematical reasoning, a tool that describes promoter activity at each time point has been implemented. Protein expression and maturation, are modelled as first-order differential equations, taking into account the degradation and maturation rates which need to be known in advance. The promoter activity is then expressed based on the measured values of fluorescence and OD with a formula derived by mathematical manipulations of the defined quantities and the differential equations that comprise the model. Continuous expressions for fluorescence and OD are obtained from Gaussian process regression. Validation of the tool with experimental data from several constructs showed the expected behaviour of promoter activities.

Keywords

• fluorescence
• proteins
• molecular biophysics
• genetics
• time series
• differential equations
• gaussian processes
• promoter activities
• fluorescent protein expression data
• repressors
• enhancers
• gene regulation
• biomass
• optical density
• coupled time-series experiment
• protein maturation
• first-order differential equations
• gaussian process regression