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Title: Generation of a platform strain for ionic liquid tolerance using adaptive laboratory evolution

Abstract

There is a need to replace petroleum-derived with sustainable feedstocks for chemical production. Certain biomass feedstocks can meet this need as abundant, diverse, and renewable resources. Specific ionic liquids (ILs) can play a role in this process as promising candidates for chemical pretreatment and deconstruction of plant-based biomass feedstocks as they efficiently release carbohydrates which can be fermented. However, the most efficient pretreatment ILs are highly toxic to biological systems, such as microbial fermentations, and hinder subsequent bioprocessing of fermentative sugars obtained from IL-treated biomass. To generate strains capable of tolerating residual ILs present in treated feedstocks, a tolerance adaptive laboratory evolution (TALE) approach was developed and utilized to improve growth of two different Escherichia coli strains, DH1 and K-12 MG1655, in the presence of two different ionic liquids, 1-ethyl-3-methylimidazolium acetate ([C 2C 1Im][OAc] ) and 1-butyl-3-methylimidazolium chloride ([C 4C 1Im]Cl). For multiple parallel replicate populations of E. coli, cells were repeatedly passed to select for improved fitness over the course of approximately 40 days. Clonal isolates were screened and the best performing isolates were subjected to whole genome sequencing. The most prevalent mutations in tolerant clones occurred in transport processes related to the functions of mdtJI, a multidrug effluxmore » pump, and yhdP, an uncharacterized transporter. Additional mutations were enriched in processes such as transcriptional regulation and nucleotide biosynthesis. Finally, the best-performing strains were compared to previously characterized tolerant strains and showed superior performance in tolerance of different IL and media combinations (i.e., cross tolerance) with robust growth at 8.5% (w/v) and detectable growth up to 11.9% (w/v) [C 2C 1Im][OAc]. The generated strains thus represent the best performing platform strains available for bioproduction utilizing IL-treated renewable substrates, and the TALE method was highly successful in overcoming the general issue of substrate toxicity and has great promise for use in tolerance engineering.« less

Authors:
 [1];  [2];  [1];  [1];  [3];  [3]; ORCiD logo [4]
  1. Technical Univ. of Denmark, Lyngby (Denmark)
  2. Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Beijing Univ. of Chemical Technology, Beijing (People's Republic of China)
  3. Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  4. Technical Univ. of Denmark, Lyngby (Denmark); Univ. of California, San Diego, CA (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1419445
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Microbial Cell Factories
Additional Journal Information:
Journal Volume: 16; Journal Issue: 1; Journal ID: ISSN 1475-2859
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Escherichia coli; Renewable feedstocks; Ionic liquids; Adaptive laboratory evolution

Citation Formats

Mohamed, Elsayed T., Wang, Shizeng, Lennen, Rebecca M., Herrgard, Markus J., Simmons, Blake A., Singer, Steven W., and Feist, Adam M. Generation of a platform strain for ionic liquid tolerance using adaptive laboratory evolution. United States: N. p., 2017. Web. doi:10.1186/s12934-017-0819-1.
Mohamed, Elsayed T., Wang, Shizeng, Lennen, Rebecca M., Herrgard, Markus J., Simmons, Blake A., Singer, Steven W., & Feist, Adam M. Generation of a platform strain for ionic liquid tolerance using adaptive laboratory evolution. United States. doi:10.1186/s12934-017-0819-1.
Mohamed, Elsayed T., Wang, Shizeng, Lennen, Rebecca M., Herrgard, Markus J., Simmons, Blake A., Singer, Steven W., and Feist, Adam M. Thu . "Generation of a platform strain for ionic liquid tolerance using adaptive laboratory evolution". United States. doi:10.1186/s12934-017-0819-1. https://www.osti.gov/servlets/purl/1419445.
@article{osti_1419445,
title = {Generation of a platform strain for ionic liquid tolerance using adaptive laboratory evolution},
author = {Mohamed, Elsayed T. and Wang, Shizeng and Lennen, Rebecca M. and Herrgard, Markus J. and Simmons, Blake A. and Singer, Steven W. and Feist, Adam M.},
abstractNote = {There is a need to replace petroleum-derived with sustainable feedstocks for chemical production. Certain biomass feedstocks can meet this need as abundant, diverse, and renewable resources. Specific ionic liquids (ILs) can play a role in this process as promising candidates for chemical pretreatment and deconstruction of plant-based biomass feedstocks as they efficiently release carbohydrates which can be fermented. However, the most efficient pretreatment ILs are highly toxic to biological systems, such as microbial fermentations, and hinder subsequent bioprocessing of fermentative sugars obtained from IL-treated biomass. To generate strains capable of tolerating residual ILs present in treated feedstocks, a tolerance adaptive laboratory evolution (TALE) approach was developed and utilized to improve growth of two different Escherichia coli strains, DH1 and K-12 MG1655, in the presence of two different ionic liquids, 1-ethyl-3-methylimidazolium acetate ([C2C1Im][OAc] ) and 1-butyl-3-methylimidazolium chloride ([C4C1Im]Cl). For multiple parallel replicate populations of E. coli, cells were repeatedly passed to select for improved fitness over the course of approximately 40 days. Clonal isolates were screened and the best performing isolates were subjected to whole genome sequencing. The most prevalent mutations in tolerant clones occurred in transport processes related to the functions of mdtJI, a multidrug efflux pump, and yhdP, an uncharacterized transporter. Additional mutations were enriched in processes such as transcriptional regulation and nucleotide biosynthesis. Finally, the best-performing strains were compared to previously characterized tolerant strains and showed superior performance in tolerance of different IL and media combinations (i.e., cross tolerance) with robust growth at 8.5% (w/v) and detectable growth up to 11.9% (w/v) [C2C1Im][OAc]. The generated strains thus represent the best performing platform strains available for bioproduction utilizing IL-treated renewable substrates, and the TALE method was highly successful in overcoming the general issue of substrate toxicity and has great promise for use in tolerance engineering.},
doi = {10.1186/s12934-017-0819-1},
journal = {Microbial Cell Factories},
number = 1,
volume = 16,
place = {United States},
year = {2017},
month = {11}
}

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    Works referencing / citing this record:

    Generation of an E. coli platform strain for improved sucrose utilization using adaptive laboratory evolution
    journal, June 2019

    • Mohamed, Elsayed T.; Mundhada, Hemanshu; Landberg, Jenny
    • Microbial Cell Factories, Vol. 18, Issue 1
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    Generation of an E. coli platform strain for improved sucrose utilization using adaptive laboratory evolution
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