CRISPR-Cas9-driven genome editing in Bacillus methanolicus MGA3

Bacillus methanolicus is a thermophilic methylotroph that uses methanol as a sustainable feedstock in biotechnological industry. Here, we developed the CRISPR-Cas9 genome editing tool for B. methanolicus MGA3. This one-plasmid system induces Cas9-mediated double-strand breaks and exploits native DNA repair: homologous recombination for scarless deletions and gene replacements, and error-prone end-joining repair for mutagenesis in the absence of a repair template. Consistent with end-joining activity, Cas9 cutting without a template resulted in reproducible small indels near the cleavage site. Using homology-directed repair, we deleted the katA and ald genes, confirmed the edits by genome sequencing, and demonstrated the expected loss of catalase and alanine dehydrogenase activities, respectively; both phenotypes were restored by complementation. For targeted gene insertion, the katA locus was replaced with mcherry, and successful integration was verified by PCR and increased mCherry fluorescence relative to the wild type. The system was further used to delete spo0A and replace it with mrpf1. The overall genome-editing efficiency exceeded 85%. This study demonstrates that the developed genome editing platform enables precise and efficient genetic modifications for metabolic engineering in B. methanolicus.