Efficient CRISPR-mediated base editing in Agrobacterium spp.

Agrobacterium spp. are important plant pathogens that are the causative agents of crown gall or hairy root disease. Their unique infection strategy depends on the delivery of part of their DNA to plant cells. This capacity converted these phytopathogens into a powerful and indispensable tool for plant genetic engineering and agricultural biotechnology. Although Agrobacterium spp. are standard tools for plant molecular biologists, current laboratory strains have remained unchanged for decades and functional gene analysis of Agrobacterium has been hampered by time-consuming mutation strategies. Here, we developed CRISPR-mediated base editing to enable the highly efficient introduction of targeted point mutations into the genomes of both Agrobacterium tumefaciens and A. rhizogenes. As an example, we generated EHA105 strains, with loss-of-function mutations in recA, that were fully functional for maize (Zea mays) transformation and confirmed the importance of rolB and rolC for hairy root development by A. rhizogenes K599. Our method is highly efficient with 9 out of 10 colonies after transformation showing edits in at least 80% of cells. The genomes of EHA105 and K599 were re-sequenced and genome-wide off-target analysis was applied to investigate the edited strains after curing of the base editor plasmid. The off-targets present were characteristic of Cas9-independent off-targeting and point to TC motifs as activity hotspots of the cytidine deaminase used. We anticipate that CRISPR-mediated base editing is the start of 'engineering the engineer', leading to improved Agrobacterium strains for more efficient plant transformation and gene editing.