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Ensemble Bayesian Analysis of Bistability in a Synthetic Transcriptional Switch

Subsoontorn, Pakpoom and Kim, Jongmin and Winfree, Erik (2012) Ensemble Bayesian Analysis of Bistability in a Synthetic Transcriptional Switch. ACS Synthetic Biology, 1 (8). pp. 299-316. ISSN 2161-5063. doi:10.1021/sb300018h. https://resolver.caltech.edu/CaltechAUTHORS:20120803-102247969

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Abstract

An overarching goal of synthetic and systems biology is to engineer and understand complex biochemical systems by rationally designing and analyzing their basic component interactions. Practically, the extent to which such reductionist approaches can be applied is unclear especially as the complexity of the system increases. Toward gradually increasing the complexity of systematically engineered systems, programmable synthetic circuits operating in cell-free in vitro environments offer a valuable testing ground for principles for the design, characterization, and analysis of complex biochemical systems. Here we illustrate this approach using in vitro transcriptional circuits (“genelets”) while developing an activatable transcriptional switch motif and configuring it as a bistable autoregulatory circuit, using just four synthetic DNA strands and three essential enzymes, bacteriophage T7 RNA polymerase, Escherichia coli ribonuclease H, and ribonuclease R. Fulfilling the promise of predictable system design, the thermodynamic and kinetic constraints prescribed at the sequence level were enough to experimentally demonstrate intended bistable dynamics for the synthetic autoregulatory switch. A simple mathematical model was constructed based on the mechanistic understanding of elementary reactions, and a Monte Carlo Bayesian inference approach was employed to find parameter sets compatible with a training set of experimental results; this ensemble of parameter sets was then used to predict a test set of additional experiments with reasonable agreement and to provide a rigorous basis for confidence in the mechanistic model. Our work demonstrates that programmable in vitro biochemical circuits can serve as a testing ground for evaluating methods for the design and analysis of more complex biochemical systems such as living cells.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1021/sb300018hDOIArticle
http://pubs.acs.org/doi/suppl/10.1021/sb300018hPublisherSupporting Information
ORCID:
AuthorORCID
Kim, Jongmin0000-0002-2713-1006
Winfree, Erik0000-0002-5899-7523
Additional Information:© 2012 American Chemical Society. Received: March 23, 2012. Publication Date (Web): June 13, 2012. This work was supported by the National Science Foundation awards 0103002, 0608889, and 0832824 (The Molecular Programming Project); the Human Frontiers Science Program award RGY0074/2006-C; and the Caltech Center for Biological Circuit Design. A preliminary version of this work appeared in ref 80. P.S., J.K., and E.W. designed research; P.S. performed experiments; P.S., J.K., and E.W. analyzed data; P.S., J.K., and E.W. wrote the manuscript. The authors declare no competing financial interest.
Funders:
Funding AgencyGrant Number
NSFCBET-0103002
NSFCBET-0608889
NSFCCF-0832824
Human Frontier Science ProgramRGY0074/2006-C
Caltech Center for Biological Circuit DesignUNSPECIFIED
Subject Keywords:in vitro; synthetic biology; systems biology; reductionism; transcriptional circuits
Issue or Number:8
DOI:10.1021/sb300018h
Record Number:CaltechAUTHORS:20120803-102247969
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20120803-102247969
Official Citation:Ensemble Bayesian Analysis of Bistability in a Synthetic Transcriptional Switch Pakpoom Subsoontorn, Jongmin Kim, and Erik Winfree ACS Synthetic Biology 2012 1 (8), 299-316 DOI: 10.1021/sb300018h
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:32911
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:03 Aug 2012 17:59
Last Modified:09 Nov 2021 21:31

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