Development of both type I–B and type II CRISPR/Cas genome editing systems in the cellulolytic bacterium Clostridium thermocellum
Abstract
The robust lignocellulose-solubilizing activity of C. thermocellum makes it a top candidate for consolidated bioprocessing for biofuel production. Genetic techniques for C. thermocellum have lagged behind model organisms thus limiting attempts to improve biofuel production. To improve our ability to engineer C. thermocellum, we characterized a native Type I-B and heterologous Type II Clustered Regularly-Interspaced Short Palindromic Repeat (CRISPR)/cas (CRISPR associated) systems. We repurposed the native Type I-B system for genome editing. We tested three thermophilic Cas9 variants (Type II) and found that GeoCas9, isolated from Geobacillus stearothermophilus, is active in C. thermocellum. We employed CRISPR-mediated homology directed repair to introduce a nonsense mutation into pyrF. For both editing systems, homologous recombination between the repair template and the genome appeared to be the limiting step. To overcome this limitation, we tested three novel thermophilic recombinases and demonstrated that exo/beta homologs, isolated from Acidithiobacillus caldus, are functional in C. thermocellum. For the Type I-B system an engineered strain, termed LL1586, yielded 40% genome editing efficiency at the pyrF locus and when recombineering machinery was expressed this increased to 71%. For the Type II GeoCas9 system, 12.5% genome editing efficiency was observed and when recombineering machinery was expressed, this increased to 94%.more »
- Authors:
- Publication Date:
- Research Org.:
- National Renewable Energy Laboratory (NREL), Golden, CO (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1576060
- Alternate Identifier(s):
- OSTI ID: 1580488
- Report Number(s):
- NREL/JA-2700-74649
Journal ID: ISSN 2214-0301; S2214030119300239; e00116; PII: S2214030119300239
- Grant/Contract Number:
- AC02–05CH11231; AC36-08GO28308
- Resource Type:
- Published Article
- Journal Name:
- Metabolic Engineering Communications
- Additional Journal Information:
- Journal Name: Metabolic Engineering Communications Journal Volume: 10 Journal Issue: C; Journal ID: ISSN 2214-0301
- Publisher:
- Elsevier
- Country of Publication:
- Netherlands
- Language:
- English
- Subject:
- 09 BIOMASS FUELS; CRISPR; type I-B; Cas9; Clostridium thermocellum; thermophilic recombineering
Citation Formats
Walker, Julie E., Lanahan, Anthony A., Zheng, Tianyong, Toruno, Camilo, Lynd, Lee R., Cameron, Jeffrey C., Olson, Daniel G., and Eckert, Carrie A. Development of both type I–B and type II CRISPR/Cas genome editing systems in the cellulolytic bacterium Clostridium thermocellum. Netherlands: N. p., 2020.
Web. doi:10.1016/j.mec.2019.e00116.
Walker, Julie E., Lanahan, Anthony A., Zheng, Tianyong, Toruno, Camilo, Lynd, Lee R., Cameron, Jeffrey C., Olson, Daniel G., & Eckert, Carrie A. Development of both type I–B and type II CRISPR/Cas genome editing systems in the cellulolytic bacterium Clostridium thermocellum. Netherlands. https://doi.org/10.1016/j.mec.2019.e00116
Walker, Julie E., Lanahan, Anthony A., Zheng, Tianyong, Toruno, Camilo, Lynd, Lee R., Cameron, Jeffrey C., Olson, Daniel G., and Eckert, Carrie A. Mon .
"Development of both type I–B and type II CRISPR/Cas genome editing systems in the cellulolytic bacterium Clostridium thermocellum". Netherlands. https://doi.org/10.1016/j.mec.2019.e00116.
@article{osti_1576060,
title = {Development of both type I–B and type II CRISPR/Cas genome editing systems in the cellulolytic bacterium Clostridium thermocellum},
author = {Walker, Julie E. and Lanahan, Anthony A. and Zheng, Tianyong and Toruno, Camilo and Lynd, Lee R. and Cameron, Jeffrey C. and Olson, Daniel G. and Eckert, Carrie A.},
abstractNote = {The robust lignocellulose-solubilizing activity of C. thermocellum makes it a top candidate for consolidated bioprocessing for biofuel production. Genetic techniques for C. thermocellum have lagged behind model organisms thus limiting attempts to improve biofuel production. To improve our ability to engineer C. thermocellum, we characterized a native Type I-B and heterologous Type II Clustered Regularly-Interspaced Short Palindromic Repeat (CRISPR)/cas (CRISPR associated) systems. We repurposed the native Type I-B system for genome editing. We tested three thermophilic Cas9 variants (Type II) and found that GeoCas9, isolated from Geobacillus stearothermophilus, is active in C. thermocellum. We employed CRISPR-mediated homology directed repair to introduce a nonsense mutation into pyrF. For both editing systems, homologous recombination between the repair template and the genome appeared to be the limiting step. To overcome this limitation, we tested three novel thermophilic recombinases and demonstrated that exo/beta homologs, isolated from Acidithiobacillus caldus, are functional in C. thermocellum. For the Type I-B system an engineered strain, termed LL1586, yielded 40% genome editing efficiency at the pyrF locus and when recombineering machinery was expressed this increased to 71%. For the Type II GeoCas9 system, 12.5% genome editing efficiency was observed and when recombineering machinery was expressed, this increased to 94%. By combining the thermophilic CRISPR system (either Type I-B or Type II) with the recombinases, we developed a new tool that allows for efficient CRISPR editing. We are now poised to enable CRISPR technologies to better engineer C. thermocellum for both increased lignocellulose degradation and biofuel production.},
doi = {10.1016/j.mec.2019.e00116},
journal = {Metabolic Engineering Communications},
number = C,
volume = 10,
place = {Netherlands},
year = {Mon Jun 01 00:00:00 EDT 2020},
month = {Mon Jun 01 00:00:00 EDT 2020}
}
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