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Title: Dynamic control of endogenous metabolism with combinatorial logic circuits

Abstract

Controlling gene expression during a bioprocess enables real-time metabolic control, coordinated cellular responses, and staging order-of-operations. Achieving this with small molecule inducers is impractical at scale and dynamic circuits are difficult to design. Here, we show that the same set of sensors can be integrated by different combinatorial logic circuits to vary when genes are turned on and off during growth. Three Escherichia coli sensors that respond to the consumption of feedstock (glucose), dissolved oxygen, and by-product accumulation (acetate) are constructed and optimized. By integrating these sensors, logic circuits implement temporal control over an 18-h period. The circuit outputs are used to regulate endogenous enzymes at the transcriptional and post-translational level using CRISPRi and targeted proteolysis, respectively. As a demonstration, two circuits are designed to control acetate production by matching their dynamics to when endogenous genes are expressed ( pta or poxB) and respond by turning off the corresponding gene. We discuss how simple circuits can be implemented to enable customizable dynamic gene regulation.

Authors:
 [1];  [1];  [1];  [1];  [1]; ORCiD logo [1]
  1. Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)
Publication Date:
Research Org.:
Univ. of Colorado, Boulder, CO (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1547417
Grant/Contract Number:  
SC0018368
Resource Type:
Accepted Manuscript
Journal Name:
Molecular Systems Biology
Additional Journal Information:
Journal Volume: 14; Journal Issue: 11; Journal ID: ISSN 1744-4292
Publisher:
Wiley
Country of Publication:
United States
Language:
English
Subject:
control theory; feedback; metabolic engineering; synthetic biology

Citation Formats

Moser, Felix, Espah Borujeni, Amin, Ghodasara, Amar N., Cameron, Ewen, Park, Yongjin, and Voigt, Christopher A. Dynamic control of endogenous metabolism with combinatorial logic circuits. United States: N. p., 2018. Web. doi:10.15252/msb.20188605.
Moser, Felix, Espah Borujeni, Amin, Ghodasara, Amar N., Cameron, Ewen, Park, Yongjin, & Voigt, Christopher A. Dynamic control of endogenous metabolism with combinatorial logic circuits. United States. doi:10.15252/msb.20188605.
Moser, Felix, Espah Borujeni, Amin, Ghodasara, Amar N., Cameron, Ewen, Park, Yongjin, and Voigt, Christopher A. Thu . "Dynamic control of endogenous metabolism with combinatorial logic circuits". United States. doi:10.15252/msb.20188605. https://www.osti.gov/servlets/purl/1547417.
@article{osti_1547417,
title = {Dynamic control of endogenous metabolism with combinatorial logic circuits},
author = {Moser, Felix and Espah Borujeni, Amin and Ghodasara, Amar N. and Cameron, Ewen and Park, Yongjin and Voigt, Christopher A.},
abstractNote = {Controlling gene expression during a bioprocess enables real-time metabolic control, coordinated cellular responses, and staging order-of-operations. Achieving this with small molecule inducers is impractical at scale and dynamic circuits are difficult to design. Here, we show that the same set of sensors can be integrated by different combinatorial logic circuits to vary when genes are turned on and off during growth. Three Escherichia coli sensors that respond to the consumption of feedstock (glucose), dissolved oxygen, and by-product accumulation (acetate) are constructed and optimized. By integrating these sensors, logic circuits implement temporal control over an 18-h period. The circuit outputs are used to regulate endogenous enzymes at the transcriptional and post-translational level using CRISPRi and targeted proteolysis, respectively. As a demonstration, two circuits are designed to control acetate production by matching their dynamics to when endogenous genes are expressed (pta or poxB) and respond by turning off the corresponding gene. We discuss how simple circuits can be implemented to enable customizable dynamic gene regulation.},
doi = {10.15252/msb.20188605},
journal = {Molecular Systems Biology},
number = 11,
volume = 14,
place = {United States},
year = {2018},
month = {11}
}

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