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Published on: March 29, 2019
Uncovering cis regulatory codes using synthetic promoter shuffling
Ali Kinkhabwala1, Călin C Guet
1Laboratory of Living Matter and Center for Studies in Physics and Biology, Rockefeller University, New York, New York, United States of America. kinkhabw@mpi-dortmund.mpg.de
Plos One
|May 1, 2008
Summary
Researchers shuffled bacterial promoter sequences to uncover how they perform logic functions. They found NOR and ANDN logic gates dominate, determined by simple regulatory codes, offering insights into biological network complexity.
Area of Science:
- Synthetic biology
- Molecular biology
- Systems biology
Background:
- Understanding transcriptional regulation in biological networks requires deciphering complex promoter logic.
- Current methods struggle to decode the computational logic of integrated molecular signals at complex promoters.
- A simple cis-regulatory code for promoter function is lacking.
Purpose of the Study:
- To synthetically shuffle regulatory elements of a bacterial promoter to explore encoded logic functions.
- To establish a map between promoter structure and logic phenotype.
- To investigate the potential of synthetic promoter shuffling as an experimental tool.
Main Methods:
- Synthetic shuffling of operator sequences binding activators and repressors in a canonical bacterial promoter.
- Construction of a library of complex promoters to explore logic regulation.
- Analysis of predominant logic functions (NOR, ANDN) and their underlying cis-regulatory codes.
Main Results:
- NOR and ANDN logic functions were found to predominate among shuffled promoters.
- A simple transcriptional cis-regulatory code, based on repressor/activator combinations, dictates these logic functions.
- Three-input versions of NOR and ANDN logics were also generated, demonstrating versatility.
- The engineered promoters exhibited a wide dynamic range of transcriptional strengths.
Conclusions:
- Synthetic promoter shuffling is an efficient method for exploring complex regulatory functions encoded by promoters.
- A direct relationship exists between promoter architecture and its logic output.
- This approach facilitates experimental testing of complex promoter functions and may aid in studying natural promoter shuffling.
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