A unified design space of synthetic stripe-forming networks

Nat Commun. 2014 Sep 23;5:4905. doi: 10.1038/ncomms5905.

Abstract

Synthetic biology is a promising tool to study the function and properties of gene regulatory networks. Gene circuits with predefined behaviours have been successfully built and modelled, but largely on a case-by-case basis. Here we go beyond individual networks and explore both computationally and synthetically the design space of possible dynamical mechanisms for 3-node stripe-forming networks. First, we computationally test every possible 3-node network for stripe formation in a morphogen gradient. We discover four different dynamical mechanisms to form a stripe and identify the minimal network of each group. Next, with the help of newly established engineering criteria we build these four networks synthetically and show that they indeed operate with four fundamentally distinct mechanisms. Finally, this close match between theory and experiment allows us to infer and subsequently build a 2-node network that represents the archetype of the explored design space.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Cloning, Molecular
  • Escherichia coli
  • Fluorescence
  • Gene Regulatory Networks / genetics*
  • Genetic Engineering / methods*
  • Models, Genetic*
  • Molecular Sequence Data
  • Plasmids / genetics
  • Reverse Transcriptase Polymerase Chain Reaction
  • Sequence Analysis, DNA
  • Synthetic Biology / methods*

Associated data

  • GENBANK/KM229376
  • GENBANK/KM229377
  • GENBANK/KM229378
  • GENBANK/KM229379
  • GENBANK/KM229380
  • GENBANK/KM229381
  • GENBANK/KM229382
  • GENBANK/KM229383
  • GENBANK/KM229384
  • GENBANK/KM229385
  • GENBANK/KM229386
  • GENBANK/KM229387
  • GENBANK/KM229388
  • GENBANK/KM229389
  • GENBANK/KM229390
  • GENBANK/KM229391