Programming gene expression with combinatorial promoters

Creators: Cox, Robert Sidney, III; Surette, Michael G.; Elowitz, Michael B.

Abstract

Promoters control the expression of genes in response to one or more transcription factors (TFs). The architecture of a promoter is the arrangement and type of binding sites within it. To understand natural genetic circuits and to design promoters for synthetic biology, it is essential to understand the relationship between promoter function and architecture. We constructed a combinatorial library of random promoter architectures. We characterized 288 promoters in Escherichia coli, each containing up to three inputs from four different TFs. The library design allowed for multiple −10 and −35 boxes, and we observed varied promoter strength over five decades. To further analyze the functional repertoire, we defined a representation of promoter function in terms of regulatory range, logic type, and symmetry. Using these results, we identified heuristic rules for programming gene expression with combinatorial promoters.

Additional Information

© 2007 EMBO and Nature Publishing Group This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits distribution, and reproduction in any medium, provided the original author and source are credited. This license does not permit commercial exploitation or the creation of derivative works without specific permission. Received 19.6.07; accepted 21.9.07. We thank Aaron White for help with library design and construction, Mercedes Paulino for help preparing figures, and Carla Davidson for plasmid pCD136. Avidgor Eldar contributed to the logic‐symmetry space formalism. T Irie, D Morris, P Sternberg, E Winfree, G Anderson, J Locke, H Garcia, R Kishony, U Alon, and C Dalal provided helpful discussions. We thank W Kim, C Vizcarra, G Seelig, and J Kim for technical assistance. RSC was partially supported by the National Physical Science Consortium and Sandia National Laboratory. MGS is supported as an Alberta Heritage Foundation for Medical Research (AHFMR) Scientist and Canada Research Chair in Microbial Gene Expression. This work was supported by NIH (grants R01GM079771 to MBE and 5P50 GM068763 to the Center for Modular Biology), HFSP, the Packard Foundation, and the Caltech Center for Biological Circuit Design.