Engineering dynamic pathway regulation using stress-response promoters

Robert H Dahl; Fuzhong Zhang; Jorge Alonso-Gutierrez; Edward Baidoo; Tanveer S Batth; Alyssa M Redding-Johanson; Christopher J Petzold; Aindrila Mukhopadhyay; Taek Soon Lee; Paul D Adams; Jay D Keasling

doi:10.1038/nbt.2689

Engineering dynamic pathway regulation using stress-response promoters

Robert H Dahl, Fuzhong Zhang, Jorge Alonso-Gutierrez, Edward Baidoo, Tanveer S Batth, Alyssa M Redding-Johanson, Christopher J Petzold, Aindrila Mukhopadhyay, Taek Soon Lee, Paul D Adams, Jay D Keasling

296 Citations (Scopus)

Abstract

Heterologous pathways used in metabolic engineering may produce intermediates toxic to the cell. Dynamic control of pathway enzymes could prevent the accumulation of these metabolites, but such a strategy requires sensors, which are largely unknown, that can detect and respond to the metabolite. Here we applied whole-genome transcript arrays to identify promoters that respond to the accumulation of toxic intermediates, and then used these promoters to control accumulation of the intermediate and improve the final titers of a desired product. We apply this approach to regulate farnesyl pyrophosphate (FPP) production in the isoprenoid biosynthetic pathway in Escherichia coli. This strategy improved production of amorphadiene, the final product, by twofold over that from inducible or constitutive promoters, eliminated the need for expensive inducers, reduced acetate accumulation and improved growth. We extended this approach to another toxic intermediate to demonstrate the broad utility of identifying novel sensor-regulator systems for dynamic regulation.

Original language	English
Journal	Nature Biotechnology
ISSN	1087-0156
DOIs	https://doi.org/10.1038/nbt.2689
Publication status	Published - Nov 2013
Externally published	Yes

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title = "Engineering dynamic pathway regulation using stress-response promoters",

abstract = "Heterologous pathways used in metabolic engineering may produce intermediates toxic to the cell. Dynamic control of pathway enzymes could prevent the accumulation of these metabolites, but such a strategy requires sensors, which are largely unknown, that can detect and respond to the metabolite. Here we applied whole-genome transcript arrays to identify promoters that respond to the accumulation of toxic intermediates, and then used these promoters to control accumulation of the intermediate and improve the final titers of a desired product. We apply this approach to regulate farnesyl pyrophosphate (FPP) production in the isoprenoid biosynthetic pathway in Escherichia coli. This strategy improved production of amorphadiene, the final product, by twofold over that from inducible or constitutive promoters, eliminated the need for expensive inducers, reduced acetate accumulation and improved growth. We extended this approach to another toxic intermediate to demonstrate the broad utility of identifying novel sensor-regulator systems for dynamic regulation.",

author = "Dahl, {Robert H} and Fuzhong Zhang and Jorge Alonso-Gutierrez and Edward Baidoo and Batth, {Tanveer S} and Redding-Johanson, {Alyssa M} and Petzold, {Christopher J} and Aindrila Mukhopadhyay and Lee, {Taek Soon} and Adams, {Paul D} and Keasling, {Jay D}",

year = "2013",

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doi = "10.1038/nbt.2689",

language = "English",

journal = "Nature Biotechnology",

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TY - JOUR

T1 - Engineering dynamic pathway regulation using stress-response promoters

AU - Dahl, Robert H

AU - Zhang, Fuzhong

AU - Alonso-Gutierrez, Jorge

AU - Baidoo, Edward

AU - Batth, Tanveer S

AU - Redding-Johanson, Alyssa M

AU - Petzold, Christopher J

AU - Mukhopadhyay, Aindrila

AU - Lee, Taek Soon

AU - Adams, Paul D

AU - Keasling, Jay D

PY - 2013/11

Y1 - 2013/11

N2 - Heterologous pathways used in metabolic engineering may produce intermediates toxic to the cell. Dynamic control of pathway enzymes could prevent the accumulation of these metabolites, but such a strategy requires sensors, which are largely unknown, that can detect and respond to the metabolite. Here we applied whole-genome transcript arrays to identify promoters that respond to the accumulation of toxic intermediates, and then used these promoters to control accumulation of the intermediate and improve the final titers of a desired product. We apply this approach to regulate farnesyl pyrophosphate (FPP) production in the isoprenoid biosynthetic pathway in Escherichia coli. This strategy improved production of amorphadiene, the final product, by twofold over that from inducible or constitutive promoters, eliminated the need for expensive inducers, reduced acetate accumulation and improved growth. We extended this approach to another toxic intermediate to demonstrate the broad utility of identifying novel sensor-regulator systems for dynamic regulation.

AB - Heterologous pathways used in metabolic engineering may produce intermediates toxic to the cell. Dynamic control of pathway enzymes could prevent the accumulation of these metabolites, but such a strategy requires sensors, which are largely unknown, that can detect and respond to the metabolite. Here we applied whole-genome transcript arrays to identify promoters that respond to the accumulation of toxic intermediates, and then used these promoters to control accumulation of the intermediate and improve the final titers of a desired product. We apply this approach to regulate farnesyl pyrophosphate (FPP) production in the isoprenoid biosynthetic pathway in Escherichia coli. This strategy improved production of amorphadiene, the final product, by twofold over that from inducible or constitutive promoters, eliminated the need for expensive inducers, reduced acetate accumulation and improved growth. We extended this approach to another toxic intermediate to demonstrate the broad utility of identifying novel sensor-regulator systems for dynamic regulation.

U2 - 10.1038/nbt.2689

DO - 10.1038/nbt.2689

M3 - Journal article

C2 - 24142050

SN - 1087-0156

JO - Nature Biotechnology

JF - Nature Biotechnology

ER -

Engineering dynamic pathway regulation using stress-response promoters

Abstract

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