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Title: Programming mRNA decay to modulate synthetic circuit resource allocation

Abstract

Synthetic circuits embedded in host cells compete with cellular processes for limited intracellular resources. Here we show how funnelling of cellular resources, after global transcriptome degradation by the sequence-dependent endoribonuclease MazF, to a synthetic circuit can increase production. Target genes are protected from MazF activity by recoding the gene sequence to eliminate recognition sites, while preserving the amino acid sequence. The expression of a protected fluorescent reporter and flux of a high-value metabolite are significantly enhanced using this genome-scale control strategy. Proteomics measurements discover a host factor in need of protection to improve resource redistribution activity. A computational model demonstrates that the MazF mRNA-decay feedback loop enables proportional control of MazF in an optimal operating regime. Transcriptional profiling of MazF-induced cells elucidates the dynamic shifts in transcript abundance and discovers regulatory design elements. Altogether, our results suggest that manipulation of cellular resource allocation is a key control parameter for synthetic circuit design.

Authors:
 [1];  [1];  [2];  [3]; ORCiD logo [3]; ORCiD logo [4]
  1. Univ. of California, Berkeley, CA (United States). California Inst. for Quantitative Biosciences, Dept. of Bioengineering
  2. Univ. of California, Berkeley, CA (United States). Energy Biosciences Inst.
  3. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Joint BioEnergy Inst. and Biological Systems and Engineering Division
  4. Univ. of California, Berkeley, CA (United States). California Inst. for Quantitative Biosciences, Dept. of Bioengineering, Energy Biosciences Inst., Environmental Genomics and Systems Biology
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1379818
Grant/Contract Number:
AC02-05CH11231
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Nature Communications
Additional Journal Information:
Journal Volume: 8; Journal ID: ISSN 2041-1723
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
60 APPLIED LIFE SCIENCES; 59 BASIC BIOLOGICAL SCIENCES; genetic circuit engineering; RNA decay; synthetic biology

Citation Formats

Venturelli, Ophelia S., Tei, Mika, Bauer, Stefan, Chan, Leanne Jade G., Petzold, Christopher J., and Arkin, Adam P. Programming mRNA decay to modulate synthetic circuit resource allocation. United States: N. p., 2017. Web. doi:10.1038/ncomms15128.
Venturelli, Ophelia S., Tei, Mika, Bauer, Stefan, Chan, Leanne Jade G., Petzold, Christopher J., & Arkin, Adam P. Programming mRNA decay to modulate synthetic circuit resource allocation. United States. doi:10.1038/ncomms15128.
Venturelli, Ophelia S., Tei, Mika, Bauer, Stefan, Chan, Leanne Jade G., Petzold, Christopher J., and Arkin, Adam P. Wed . "Programming mRNA decay to modulate synthetic circuit resource allocation". United States. doi:10.1038/ncomms15128. https://www.osti.gov/servlets/purl/1379818.
@article{osti_1379818,
title = {Programming mRNA decay to modulate synthetic circuit resource allocation},
author = {Venturelli, Ophelia S. and Tei, Mika and Bauer, Stefan and Chan, Leanne Jade G. and Petzold, Christopher J. and Arkin, Adam P.},
abstractNote = {Synthetic circuits embedded in host cells compete with cellular processes for limited intracellular resources. Here we show how funnelling of cellular resources, after global transcriptome degradation by the sequence-dependent endoribonuclease MazF, to a synthetic circuit can increase production. Target genes are protected from MazF activity by recoding the gene sequence to eliminate recognition sites, while preserving the amino acid sequence. The expression of a protected fluorescent reporter and flux of a high-value metabolite are significantly enhanced using this genome-scale control strategy. Proteomics measurements discover a host factor in need of protection to improve resource redistribution activity. A computational model demonstrates that the MazF mRNA-decay feedback loop enables proportional control of MazF in an optimal operating regime. Transcriptional profiling of MazF-induced cells elucidates the dynamic shifts in transcript abundance and discovers regulatory design elements. Altogether, our results suggest that manipulation of cellular resource allocation is a key control parameter for synthetic circuit design.},
doi = {10.1038/ncomms15128},
journal = {Nature Communications},
number = ,
volume = 8,
place = {United States},
year = {Wed Apr 26 00:00:00 EDT 2017},
month = {Wed Apr 26 00:00:00 EDT 2017}
}

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