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Open Access Research article

Integration of transcriptional inputs at promoters of the arabinose catabolic pathway

Carla J Davidson1*, Atul Narang2 and Michael G Surette3

Author Affiliations

1 University of Calgary, Department of Biology, BI376b 2500 University Dr. N.W., Calgary, AB. T2N 1N4 Canada

2 Department of Biochemical Engineering & Biotechnology, Indian Institute of Technology, Hauz Khas, New Delhi 110 016, India

3 University of Calgary, Department of Microbiology and Infectious Diseases, Room 268 Heritage Medical Research Building, 3330 Hospital Drive NW, Calgary, AB T2N 4N1 Canada

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BMC Systems Biology 2010, 4:75  doi:10.1186/1752-0509-4-75

Published: 2 June 2010

Abstract

Background

Most modelling efforts of transcriptional networks involve estimations of in vivo concentrations of components, binding affinities and reaction rates, derived from in vitro biochemical assays. These assays are difficult and in vitro measurements may not approximate actual in vivo conditions. Alternatively, changes in transcription factor activity can be estimated by using partially specified models which estimate the "hidden functions" of transcription factor concentration changes; however, non-unique solutions are a potential problem. We have applied a synthetic biology approach to develop reporters that are capable of measuring transcription factor activity in vivo in real time. These synthetic reporters are comprised of a constitutive promoter with an operator site for the specific transcription factor immediately downstream. Thus, increasing transcription factor activity is measured as repression of expression of the transcription factor reporter. Measuring repression instead of activation avoids the complications of non-linear interactions between the transcription factor and RNA polymerase which differs at each promoter.

Results

Using these reporters, we show that a simple model is capable of determining the rules of integration for multiple transcriptional inputs at the four promoters of the arabinose catabolic pathway. Furthermore, we show that despite the complex and non-linear changes in cAMP-CRP activity in vivo during diauxic shift, the synthetic transcription factor reporters are capable of measuring real-time changes in transcription factor activity, and the simple model is capable of predicting the dynamic behaviour of the catabolic promoters.

Conclusions

Using a synthetic biology approach we show that the in vivo activity of transcription factors can be quantified without the need for measuring intracellular concentrations, binding affinities and reaction rates. Using measured transcription factor activity we show how different promoters can integrate common transcriptional inputs, resulting in distinct expression patterns. The data collected show that cAMP levels in vivo are dynamic and agree with observations showing that cAMP levels show a transient pulse during diauxic shift.