Fragment Exchange Plasmid Tools for CRISPR/Cas9-Mediated Gene Integration and Protease Production in Bacillus subtilis

• Published in: Applied and environmental microbiology Vol. 87; no. 1; pp. 1 - 14
• Main Authors: García-Moyano, Antonio, Larsen, Øivind, Gaykawad, Sushil, Christakou, Eleni, Boccadoro, Catherine, Puntervoll, Pål, Bjerga, Gro Elin Kjæreng
• Format: Journal Article
• Language: English
• Published: United States American Society for Microbiology 17.12.2020
• Subjects: Bacillus; Bacillus subtilis; Bacillus subtilis - enzymology; Bacillus subtilis - genetics; Biotechnology; Cloning; Cloning vectors; CRISPR; CRISPR-Cas Systems; Customization; E coli; Editing; Enzymes; Exchanging; Expression vectors; Fermentation; Gene Editing; Genome editing; Genomes; Genomics; Immune system; Integration; Loci; Peptide Hydrolases - genetics; Peptide Hydrolases - metabolism; Plasmids; Plasmids - genetics; Plasmids - metabolism; Protease; Proteinase; Sporulation; Strategy; Subtilisin; protease; CRISPR; genome editing; Bacillus subtilis; FX cloning; subtilisin; microbial fermentation
• ISSN: 0099-2240; 1098-5336
• DOI: 10.1128/AEM.02090-20

Since its discovery as part of the bacterial adaptative immune system, CRISPR/Cas has emerged as the most promising tool for targeted genome editing over the past few years. Various tools for genome editing in have recently been developed, expanding and simplifying its potential development as an industrial species. A collection of vectors compatible with high-throughput (HTP) fragment exchange (FX) cloning for heterologous expression in and was previously developed. This vector catalogue was through this work supplemented with editing plasmids for genome engineering in by adapting two CRISPR/Cas plasmids to the cloning technology. The customized tools allow versatile editing at any chosen genomic position (single-plasmid strategy) or at a fixed genomic locus (double-plasmid strategy). The single-plasmid strategy was validated by deleting the gene, which has an essential role in sporulation. Using the double-plasmid strategy, we demonstrate the quick transition from plasmid-based subtilisin expression to the stable integration of the gene into the locus of a seven-protease-deficient KO7 strain. The newly engineered strain allowed the successful production of a functional enzyme. The customized tools provide improvements to the cloning procedure, should be useful for versatile genomic engineering, and contribute to a cloning platform for a quick transition from HTP enzyme expression to production through the fermentation of industrially relevant and related strains. We complemented a cloning platform with new editing plasmids that allow a quick transition from high-throughput cloning and the expression of new enzymes to the stable integration of genes for the production of enzymes through fermentation. We present two systems for the effective assembly cloning of any genome-editing cassette that shortens the engineering procedure to obtain the final editing constructs. The utility of the customized tools is demonstrated by disrupting ' capacity to sporulate and by introducing the stable expression of subtilisin. The tools should be useful to engineer strains by a variety of recombination events to ultimately improve the application range of this industry-relevant host.