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Design and implementation of three incoherent feed-forward motif based biological concentration sensors

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Systems and Synthetic Biology

Abstract

Synthetic biology is a useful tool to investigate the dynamics of small biological networks and to assess our capacity to predict their behavior from computational models. In this work we report the construction of three different synthetic networks in Escherichia coli based upon the incoherent feed-forward loop architecture. The steady state behavior of the networks was investigated experimentally and computationally under different mutational regimes in a population based assay. Our data shows that the three incoherent feed-forward networks, using three different macromolecular inhibitory elements, reproduce the behavior predicted from our computational model. We also demonstrate that specific biological motifs can be designed to generate similar behavior using different components. In addition we show how it is possible to tune the behavior of the networks in a predicable manner by applying suitable mutations to the inhibitory elements.

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Abbreviations

EC:

Elongation complex

FFL:

Feed-forward loop

GFP:

Green fluorescent protein

IPTG:

Isopropyl-β-d-thiogalactopyranoside

LB:

Luria broth

ORF:

Open reading frame

PCR:

Polymerase chain reaction

RBS:

Ribosome binding site

T7-RNAP:

T7 RNA polymerase T7-RNAP

SAM:

S-Adenosyl methionine

SBW:

Systems biology workbench

TE:

Translational efficiency

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Acknowledgements

This work was supported by a grant from the National Science Foundation (Id 0432190). The GFP was kindly donated by Drew Endy form the Biobricks repository. We would also like to acknowledge useful discussions with Vijay Chickarmane.

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Authors and Affiliations

  1. Keck Graduate Institute, Claremont, CA, 91711, USA

    Robert Entus & Brian Aufderheide

  2. Department of Bioengineering, University of Washington, William H. Foege Building, Box 355061, Seattle, WA, 98195, USA

    Herbert M. Sauro

Authors
  1. Robert Entus
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  2. Brian Aufderheide
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  3. Herbert M. Sauro
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Corresponding author

Correspondence to Herbert M. Sauro.

Additional information

Brian Aufderheide provided material support.

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Entus, R., Aufderheide, B. & Sauro, H.M. Design and implementation of three incoherent feed-forward motif based biological concentration sensors. Syst Synth Biol 1, 119–128 (2007). https://doi.org/10.1007/s11693-007-9008-6

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  • DOI: https://doi.org/10.1007/s11693-007-9008-6

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