Gene Circuit Performance Characterization and Resource Usage in a Cell-Free "Breadboard"

ACS Synth Biol. 2014 Jun 20;3(6):416-25. doi: 10.1021/sb400203p. Epub 2014 Apr 7.

Abstract

The many successes of synthetic biology have come in a manner largely different from those in other engineering disciplines; in particular, without well-characterized and simplified prototyping environments to play a role analogous to wind-tunnels in aerodynamics and breadboards in electrical engineering. However, as the complexity of synthetic circuits increases, the benefits--in cost savings and design cycle time--of a more traditional engineering approach can be significant. We have recently developed an in vitro "breadboard" prototyping platform based on E. coli cell extract that allows biocircuits to operate in an environment considerably simpler than, but functionally similar to, in vivo. The simplicity of this system makes it a promising tool for rapid biocircuit design and testing, as well as for probing fundamental aspects of gene circuit operation normally masked by cellular complexity. In this work, we characterize the cell-free breadboard using real-time and simultaneous measurements of transcriptional and translational activities of a small set of reporter genes and a transcriptional activation cascade. We determine the effects of promoter strength, gene concentration, and nucleoside triphosphate concentration on biocircuit properties, and we isolate the specific contributions of essential biomolecular resources-core RNA polymerase and ribosomes-to overall performance. Importantly, we show how limits on resources, particularly those involved in translation, are manifested as reduced expression in the presence of orthogonal genes that serve as additional loads on the system.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Aptamers, Nucleotide / chemistry
  • Aptamers, Nucleotide / genetics
  • Cell-Free System
  • DNA / chemistry
  • DNA / genetics
  • DNA-Directed RNA Polymerases / genetics
  • Escherichia coli / genetics
  • Gene Regulatory Networks*
  • Genes, Reporter
  • Genes, Synthetic*
  • Molecular Sequence Data
  • Plasmids / chemistry
  • Plasmids / genetics
  • Promoter Regions, Genetic
  • RNA, Messenger / chemistry
  • RNA, Messenger / genetics
  • Ribosomes / genetics
  • Synthetic Biology
  • Transcription, Genetic
  • Transcriptional Activation

Substances

  • Aptamers, Nucleotide
  • RNA, Messenger
  • DNA
  • DNA-Directed RNA Polymerases