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

Julie E Walker; Anthony A Lanahan; Tianyong Zheng; Camilo Toruno; Lee R Lynd; Jeffrey C Cameron; Daniel G Olson; Carrie A Eckert

doi:10.1016/j.mec.2019.e00116

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

Metab Eng Commun. 2019 Nov 28:10:e00116. doi: 10.1016/j.mec.2019.e00116. eCollection 2020 Jun.

Authors

Julie E Walker^{1

2}, Anthony A Lanahan^{2

3}, Tianyong Zheng^{2

3}, Camilo Toruno^{2

3}, Lee R Lynd^{2

3}, Jeffrey C Cameron^{1

2

4

5}, Daniel G Olson^{2

3}, Carrie A Eckert^{1

2

5}

Affiliations

¹ Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO, 80303, USA.
² Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA.
³ Thayer School of Engineering, Dartmouth College, Hanover, NH, 03755, USA.
⁴ Department of Biochemistry, University of Colorado, Boulder, CO, 80303, USA.
⁵ National Renewable Energy Laboratory, Biosciences Center, Golden, USA.

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%. 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.

Keywords: 5-FOA, 5-fluoroorotic acid; CFU, colony forming unit; CRISPR; CRISPR/Cas, Clustered Regularly-Interspaced Short Palindromic Repeat/CRISPR associated; Cas9; Cas9n, nickase Cas9; Clostridium thermocellum; HDR, homology-directed repair; HR, homologous recombination; PAM, protospacer adjacent motif; RNP, Cas9-sgRNA ribonucleoprotein; Thermophilic recombineering; Tm, thiamphenicol; Type I–B; sgRNA, single guide RNA.