Fig. 4: Targeted base editing of pathogenic E. coli and K. pneumoniae strains in vitro using a non-replicative DNA payload.
From: In situ targeted base editing of bacteria in the mouse gut
a, MOI-dependent cytosine base editing of target genes clbH, clbJ and cnf1 in strain UTI89 using a vector harbouring the λ-K1F STF chimera and gpJ 1A2. The CBE inserts a premature stop codon into the target genes. b, MOI-dependent cytosine base editing of target genes fimH, fimK and aph(3′)-Ia in K. pneumoniae ST258 using a vector harbouring the λ-KL106 STF chimera and gpJ A8. The CBE inserts a premature stop codon into the target genes. c, MOI-dependent adenine base editing of the start codon of csgA (ATG to ACG) in strain TN03 using a vector harbouring the λ-K5 STF chimera and gpJ A8. d, Next-generation sequencing analysis of on- and off-target adenine base editing (ABE8e, plasmid p2515) in TN03-csgA in vitro. The frequency of mismatches in Illumina sequencing data is shown for all 20 base pair subsequences with an NGG PAM in the reference genome with up to seven mismatches to the target sequence, including up to two in the ten PAM-proximal nucleotides. Bars represent mismatch frequency of the base with the highest frequency in each off-target. The sequence, coordinates and neighbouring genes of each off-target are listed in Supplementary Data 2. Data shown for two biological replicates of samples treated with either ABE or control. Base-editing experiments shown in a–c were performed in duplicate (1 and 2).
