A MATLAB toolbox for modeling genetic circuits in cell-free systems

Creators: Singhal, Vipul; Tuza, Zoltan A.; Sun, Zachary Z.; Murray, Richard M.

Abstract

We introduce a MATLAB-based simulation toolbox, called txtlsim, for an Escherichia coli-based Transcription–Translation (TX–TL) system. This toolbox accounts for several cell-free-related phenomena, such as resource loading, consumption and degradation, and in doing so, models the dynamics of TX–TL reactions for the entire duration of solution phase batch-mode experiments. We use a Bayesian parameter inference approach to characterize the reaction rate parameters associated with the core transcription, translation and mRNA degradation mechanics of the toolbox, allowing it to reproduce constitutive mRNA and protein-expression trajectories. We demonstrate the use of this characterized toolbox in a circuit behavior prediction case study for an incoherent feed-forward loop.

Additional Information

© The Author(s) 2021. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited.v Received: 11 August 2020; Revision received: 07 December 2020; Accepted: 23 December 2020; Published: 05 February 2021. We thank Kyle Martin, Shaobin Guo and Clarmyra Hayes for laboratory assistance, and Vincent Noireaux and Michael Jewett for advice on extract preparation methods. We thank Anandh Swaminathan, William Poole and Samuel Clamons for useful discussions about the computational methodology. This material is based upon work supported in part by the Defense Advanced Research Projects Agency (DARPA/MTO) Living Foundries program, contract number HR0011-12-C-0065 (DARPA/CMO); the Air Force Office of Scientific Research, grant number FA9550-14-1-0060; and DARPA SBIR contract W911NF-16-P-0003 (Caltech subcontract from Synvitrobio, Inc.), and a Caltech Grubstake Grant. V.S. was supported by the National Science Scholarship (NSS-PhD), Agency for Science, Technology, and Research (A*STAR), Singapore. Z.A.T. was supported by the Fulbright Scholarship. Z.Z.S. was supported by a UCLA/Caltech Medical Scientist Training Program fellowship, and a National Defense Science and Engineering Graduate fellowship. The views and conclusions contained in this document are those of the authors and should not be interpreted as representing official policies, either expressly or implied, of the Defense Advanced Research Projects Agency or the U.S. Government. Competing interests: V.S. and Z.A.T. declare no conflicts of interest. R.M.M. and Z.Z.S. declare a conflict of interest: R.M.M. and Z.Z.S. hold ownership in Tierra Biosciences (formerly Synvitrobio). Author contributions statement: R.M.M. conceived of the txtlsim toolbox, and V.S., Z.A.T. and R.M.M. wrote it. Z.Z.S. conceived of the experiments and collected the data, and V.S. conceived of and performed the parameter inference strategy. V.S. wrote the manuscript. All authors edited it. Code, data and plasmid availability: The code for this toolbox is available at https://github.com/vipulsinghal02/txtlsim_buildacell, along with multiple tutorials, and scripts to download the data and generate the figures in both the paper and the supplementary information. Supplementary section S1 gives information on the plasmids and their availability.

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Published - ysab007.pdf

Submitted - 2020.08.05.237990v1.full.pdf

Supplemental Material - ysab007_supplementary_data.zip

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