Development of both type I–B and type II CRISPR/Cas genome editing systems in the cellulolytic bacterium Clostridium thermocellum

• Published in: Metabolic engineering communications Vol. 10; no. C; p. e00116
• Main Authors: Walker, Julie E., Lanahan, Anthony A., Zheng, Tianyong, Toruno, Camilo, Lynd, Lee R., Cameron, Jeffrey C., Olson, Daniel G., Eckert, Carrie A.
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.06.2020; Elsevier
• Subjects: 09 BIOMASS FUELS; Acidithiobacillus caldus; bioprocessing; Cas9; cellulolytic bacteria; Clostridium thermocellum; CRISPR; CRISPR-Cas systems; fuel production; gene editing; genetic techniques and protocols; genome; Geobacillus stearothermophilus; homologous recombination; lignocellulose; loci; nonsense mutation; recombinases; Thermophilic recombineering; Type I–B; 5-FOA; CRISPR; Type I–B; HR; CFU; Clostridium thermocellum; sgRNA; RNP; HDR; Cas9n; Thermophilic recombineering; Tm; Cas9; CRISPR/Cas; PAM; HDR, homology-directed repair; RNP, Cas9-sgRNA ribonucleoprotein; CRISPR/Cas, Clustered Regularly-Interspaced Short Palindromic Repeat/CRISPR associated; PAM, protospacer adjacent motif; HR, homologous recombination; sgRNA, single guide RNA; 5-FOA, 5-fluoroorotic acid; Tm, thiamphenicol; CFU, colony forming unit; Cas9n, nickase Cas9
• ISSN: 2214-0301; 2214-0301
• DOI: 10.1016/j.mec.2019.e00116

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. •The native CRISPR Type I–B system was characterized in C. thermocellum.•A thermophilic CRISPR-Cas9 system was demonstrated in C. thermocellum.•Thermophilic recombineering homologs were identified for use in C. thermocellum.•Thermophilic CRISPR and recombineering systems combined improved editing efficiency.