Synthetic negative feedback circuits using engineered small RNAs

Kelly, Ciarán, Harris, Andreas W. K., Steel, Harrison, Hancock, Edward J., Heap, John T. and Papachristodoulou, Antonis (2018) Synthetic negative feedback circuits using engineered small RNAs. Nucleic Acids Research, 46 (18). pp. 9875-9889. ISSN 0305-1048

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Official URL: https://doi.org/10.1093/nar/gky828

Abstract

Negative feedback is known to enable biological and man-made systems to perform reliably in the face of uncertainties and disturbances. To date, synthetic biological feedback circuits have primarily relied upon protein-based, transcriptional regulation to control circuit output. Small RNAs (sRNAs) are non-coding RNA molecules that can inhibit translation of target messenger RNAs (mRNAs). In this work, we modelled, built and validated two synthetic negative feedback circuits that use rationally-designed sRNAs for the first time. The first circuit builds upon the well characterised tet-based autorepressor, incorporating an externally-inducible sRNA to tune the effective feedback strength. This allows more precise fine-tuning of the circuit output in contrast to the sigmoidal, steep input–output response of the autorepressor alone. In the second circuit, the output is a transcription factor that induces expression of an sRNA, which inhibits translation of the mRNA encoding the output, creating direct, closed-loop, negative feedback. Analysis of the noise profiles of both circuits showed that the use of sRNAs did not result in large increases in noise. Stochastic and deterministic modelling of both circuits agreed well with experimental data. Finally, simulations using fitted parameters allowed dynamic attributes of each circuit such as response time and disturbance rejection to be investigated.

Item Type: Article
Subjects: C100 Biology
C700 Molecular Biology, Biophysics and Biochemistry
F100 Chemistry
H800 Chemical, Process and Energy Engineering
Department: Faculties > Health and Life Sciences > Applied Sciences
Depositing User: Elena Carlaw
Date Deposited: 25 Sep 2019 15:38
Last Modified: 21 Nov 2019 14:00
URI: http://nrl.northumbria.ac.uk/id/eprint/40854

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