Synthesis of orthogonal transcription-translation networks
- 26 May 2009
- journal article
- research article
- Published by Proceedings of the National Academy of Sciences in Proceedings of the National Academy of Sciences of the United States of America
- Vol. 106 (21), 8477-8482
- https://doi.org/10.1073/pnas.0900267106
Abstract
Orthogonal, parallel and independent, systems are one key foundation for synthetic biology. The synthesis of orthogonal systems that are uncoupled from evolutionary constraints, and selectively abstracted from cellular regulation, is an emerging approach to making biology more amenable to engineering. Here, we combine orthogonal transcription by T7 RNA polymerase and translation by orthogonal ribosomes (O-ribosomes), creating an orthogonal gene expression pathway in Escherichia coli. We design and implement compact, orthogonal gene expression networks. In particular we focus on creating transcription–translation feed-forward loops (FFLs). The transcription–translation FFLs reported cannot be created by using the cells' gene expression machinery and introduce information-processing delays on the order of hours into gene expression. We refactor the rRNA operon, uncoupling the synthesis of the orthogonal 16S rRNA for the O-ribosome from the synthesis and processing of the rest of the rRNA operon, thereby defining a minimal module that can be added to the cell for O-ribosome production. The minimal O-ribosome permits the rational alteration of the delay in an orthogonal gene expression FFL. Overall this work demonstrates that system-level dynamic properties are amenable to rational manipulation and design in orthogonal systems. In the future this system may be further evolved and tuned to provide a spectrum of tailored dynamics in gene expression and investigate the effects of delays in cellular decision-making processes.Keywords
This publication has 34 references indexed in Scilit:
- Synthetic biology: discovering new worlds and new wordsEMBO Reports, 2008
- Computational design of orthogonal ribosomesNucleic Acids Research, 2008
- Evolved orthogonal ribosomes enhance the efficiency of synthetic genetic code expansionNature Biotechnology, 2007
- Synthetic biology: promises and challengesMolecular Systems Biology, 2007
- Environmental signal integration by a modular AND gateMolecular Systems Biology, 2007
- Modular approaches to expanding the functions of living matterNature Chemical Biology, 2006
- Refactoring bacteriophage T7Molecular Systems Biology, 2005
- The Engineering of Gene Regulatory NetworksAnnual Review of Biomedical Engineering, 2003
- Specific binding of monomeric bacteriophage T3 and T7 RNA polymerases to their respective cognate promoters requires the initiating ribonucleoside triphosphate (GTP)Journal of Molecular Biology, 1986
- Gene organization and primary structure of a ribosomal RNA operon from Escherichia coliJournal of Molecular Biology, 1981