Building a genome engineering toolbox in nonmodel prokaryotic microbes

Emily Freed; Jacob Fenster; Sharon L. Smolinski; Julie Walker; Calvin A. Henard; Ryan Gill; Carrie A. Eckert

doi:10.1002/bit.26727

Building a genome engineering toolbox in nonmodel prokaryotic microbes

Emily Freed, Jacob Fenster, Sharon L. Smolinski, Julie Walker, Calvin A. Henard, Ryan Gill, Carrie A. Eckert

Research output: Contribution to journal › Review article › peer-review

19 Scopus citations

Abstract

The realization of a sustainable bioeconomy requires our ability to understand and engineer complex design principles for the development of platform organisms capable of efficient conversion of cheap and sustainable feedstocks (e.g., sunlight, CO ₂ , and nonfood biomass) into biofuels and bioproducts at sufficient titers and costs. For model microbes, such as Escherichia coli, advances in DNA reading and writing technologies are driving the adoption of new paradigms for engineering biological systems. Unfortunately, microbes with properties of interest for the utilization of cheap and renewable feedstocks, such as photosynthesis, autotrophic growth, and cellulose degradation, have very few, if any, genetic tools for metabolic engineering. Therefore, it is important to develop “design rules” for building a genetic toolbox for novel microbes. Here, we present an overview of our current understanding of these rules for the genetic manipulation of prokaryotic microbes and the available genetic tools to expand our ability to genetically engineer nonmodel systems.

Original language	English
Pages (from-to)	2120-2138
Number of pages	19
Journal	Biotechnology and Bioengineering
Volume	115
Issue number	9
DOIs	https://doi.org/10.1002/bit.26727
State	Published - Sep 2018
Externally published	Yes

Funding

(C. H., E. F., S. S., and C. E.); a University of Colorado Renewable and Sustainable Energy Institute Seed Grant (J. F.); and the Office of Science Biological and Environmental Research Program through a Biosystems Design project and the Center for Bioenergy Innovation (C. E., R. G., E. F., and J. F.). The Center for Bioenergy Innovation is a U.S. Department of Energy Bioenergy Research Center supported by the Office of Biological and Environmental Research in the DOE Office of Science. The U.S. Government retains and the publisher, by accepting the article for publication, acknowledges that the U.S. Government retains a nonexclusive, paid‐up, irrevocable, worldwide license to publish or reproduce the published form of this work, or allow others to do so, for U.S. Government purposes. This study was supported by the U.S. Department of Energy Office of Energy Efficiency and Renewable Energy Bioenergy Technologies (C. H., E. F., S. S., and C. E.); a University of Colorado Renewable and Sustainable Energy Institute Seed Grant (J. F.); and the Office of Science Biological and Environmental Research Program through a Biosystems Design project and the Center for Bioenergy Innovation (C. E., R. G., E. F., and J. F.). The Center for Bioenergy Innovation is a U.S. Department of Energy Bioenergy Research Center supported by the Office of Biological and Environmental Research in the DOE Office of Science. The U.S. Government retains and the publisher, by accepting the article for publication, acknowledges that the U.S. Government retains a nonexclusive, paid-up, irrevocable, worldwide license to publish or reproduce the published form of this work, or allow others to do so, for U.S. Government purposes. Office of Energy Efficiency and Renewable Energy, Grant/Award Number: Engineering Thermophiles to Produce Drop‐in Biofue; Biological and Environmental Research, Grant/Award Numbers: Design and engineering of synthetic control archit, Center for Bioenergy Innovation (CBI); University of Colorado Renewable and Sustainable Energy Institute Seed Grant This study was supported by the U.S. Department of Energy Office of

Funders	Funder number
DOE Office of Science
Office of Biological and Environmental Research
Office of Science Biological and Environmental Research program
U.S. Department of Energy Bioenergy Research Center
U.S. Department of Energy Office of Energy Efficiency and Renewable Energy Bioenergy Technologies
U.S. Government
University of Colorado Renewable and Sustainable Energy Institute
University of Colorado Renewable and Sustainable Energy Institute Seed Grant
U.S. Department of Energy
Office of Science
Office of Energy Efficiency and Renewable Energy
Biological and Environmental Research
Center for Bioenergy Innovation

Keywords

CRISPR
bioengineering
genetic tools
genome editing
genome engineering
transformation

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1002/bit.26727

Cite this

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title = "Building a genome engineering toolbox in nonmodel prokaryotic microbes",

abstract = " The realization of a sustainable bioeconomy requires our ability to understand and engineer complex design principles for the development of platform organisms capable of efficient conversion of cheap and sustainable feedstocks (e.g., sunlight, CO 2 , and nonfood biomass) into biofuels and bioproducts at sufficient titers and costs. For model microbes, such as Escherichia coli, advances in DNA reading and writing technologies are driving the adoption of new paradigms for engineering biological systems. Unfortunately, microbes with properties of interest for the utilization of cheap and renewable feedstocks, such as photosynthesis, autotrophic growth, and cellulose degradation, have very few, if any, genetic tools for metabolic engineering. Therefore, it is important to develop “design rules” for building a genetic toolbox for novel microbes. Here, we present an overview of our current understanding of these rules for the genetic manipulation of prokaryotic microbes and the available genetic tools to expand our ability to genetically engineer nonmodel systems.",

keywords = "CRISPR, bioengineering, genetic tools, genome editing, genome engineering, transformation",

author = "Emily Freed and Jacob Fenster and Smolinski, {Sharon L.} and Julie Walker and Henard, {Calvin A.} and Ryan Gill and Eckert, {Carrie A.}",

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year = "2018",

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doi = "10.1002/bit.26727",

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AU - Fenster, Jacob

AU - Smolinski, Sharon L.

AU - Walker, Julie

AU - Henard, Calvin A.

AU - Gill, Ryan

AU - Eckert, Carrie A.

PY - 2018/9

Y1 - 2018/9

N2 - The realization of a sustainable bioeconomy requires our ability to understand and engineer complex design principles for the development of platform organisms capable of efficient conversion of cheap and sustainable feedstocks (e.g., sunlight, CO 2 , and nonfood biomass) into biofuels and bioproducts at sufficient titers and costs. For model microbes, such as Escherichia coli, advances in DNA reading and writing technologies are driving the adoption of new paradigms for engineering biological systems. Unfortunately, microbes with properties of interest for the utilization of cheap and renewable feedstocks, such as photosynthesis, autotrophic growth, and cellulose degradation, have very few, if any, genetic tools for metabolic engineering. Therefore, it is important to develop “design rules” for building a genetic toolbox for novel microbes. Here, we present an overview of our current understanding of these rules for the genetic manipulation of prokaryotic microbes and the available genetic tools to expand our ability to genetically engineer nonmodel systems.

AB - The realization of a sustainable bioeconomy requires our ability to understand and engineer complex design principles for the development of platform organisms capable of efficient conversion of cheap and sustainable feedstocks (e.g., sunlight, CO 2 , and nonfood biomass) into biofuels and bioproducts at sufficient titers and costs. For model microbes, such as Escherichia coli, advances in DNA reading and writing technologies are driving the adoption of new paradigms for engineering biological systems. Unfortunately, microbes with properties of interest for the utilization of cheap and renewable feedstocks, such as photosynthesis, autotrophic growth, and cellulose degradation, have very few, if any, genetic tools for metabolic engineering. Therefore, it is important to develop “design rules” for building a genetic toolbox for novel microbes. Here, we present an overview of our current understanding of these rules for the genetic manipulation of prokaryotic microbes and the available genetic tools to expand our ability to genetically engineer nonmodel systems.

KW - CRISPR

KW - bioengineering

KW - genetic tools

KW - genome editing

KW - genome engineering

KW - transformation

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ER -

Building a genome engineering toolbox in nonmodel prokaryotic microbes

Abstract

Funding

Keywords

UN SDGs

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