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Title: Building a genome engineering toolbox in nonmodel prokaryotic microbes


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, CO2, non-food biomass) to biofuels and bioproducts at sufficient titers and costs. For model microbes such as E. coli, advances in DNA reading and writing technologies are driving 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 begin 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 available genetic tools to expand our ability to genetically engineer non-model systems.

 [1];  [2];  [3];  [2];  [3]; ORCiD logo [1]; ORCiD logo [1]
  1. National Renewable Energy Lab. (NREL), Golden, CO (United States); Univ. of Colorado, Boulder, CO (United States)
  2. Univ. of Colorado, Boulder, CO (United States)
  3. National Renewable Energy Lab. (NREL), Golden, CO (United States)
Publication Date:
Research Org.:
National Renewable Energy Lab. (NREL), Golden, CO (United States); Univ. of Colorado, Boulder, CO (United States)
Sponsoring Org.:
USDOE Office of Energy Efficiency and Renewable Energy (EERE); USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
Alternate Identifier(s):
OSTI ID: 1439401; OSTI ID: 1558846
Report Number(s):
Journal ID: ISSN 0006-3592
Grant/Contract Number:  
AC36-08GO28308; Engineering Thermophiles to Produce Drop‐in Biofue; Design and engineering of synthetic control archit; Center for Bioenergy Innovation (CBI); SC0018368
Resource Type:
Accepted Manuscript
Journal Name:
Biotechnology and Bioengineering
Additional Journal Information:
Journal Volume: 115; Journal Issue: 9; Journal ID: ISSN 0006-3592
Country of Publication:
United States
09 BIOMASS FUELS; bioengineering; genetic tools; genome editing; genome engineering; CRISPR; transformation

Citation Formats

Freed, Emily, Fenster, Jacob, Smolinski, Sharon L., Walker, Julie, Henard, Calvin A., Gill, Ryan, and Eckert, Carrie A. Building a genome engineering toolbox in nonmodel prokaryotic microbes. United States: N. p., 2018. Web. doi:10.1002/bit.26727.
Freed, Emily, Fenster, Jacob, Smolinski, Sharon L., Walker, Julie, Henard, Calvin A., Gill, Ryan, & Eckert, Carrie A. Building a genome engineering toolbox in nonmodel prokaryotic microbes. United States. doi:
Freed, Emily, Fenster, Jacob, Smolinski, Sharon L., Walker, Julie, Henard, Calvin A., Gill, Ryan, and Eckert, Carrie A. Fri . "Building a genome engineering toolbox in nonmodel prokaryotic microbes". United States. doi:
title = {Building a genome engineering toolbox in nonmodel prokaryotic microbes},
author = {Freed, Emily and Fenster, Jacob and Smolinski, Sharon L. and Walker, Julie and Henard, Calvin A. and Gill, Ryan and Eckert, Carrie A.},
abstractNote = {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, CO2, non-food biomass) to biofuels and bioproducts at sufficient titers and costs. For model microbes such as E. coli, advances in DNA reading and writing technologies are driving 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 begin 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 available genetic tools to expand our ability to genetically engineer non-model systems.},
doi = {10.1002/bit.26727},
journal = {Biotechnology and Bioengineering},
number = 9,
volume = 115,
place = {United States},
year = {2018},
month = {5}

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