Fig. 1: Mechanism of cytidine modification and editing scope in Pseudomonas species.

A Structure of the cytidine base editor (CBE). A nicking Cas9 (nCas9) is guided by a single guide RNA (sgRNA) to the cognate protospacer sequence. Upon forming a heteroduplex between the spacer region of the gRNA and its target sequence, the complementary DNA strand becomes exposed. A cytidine deaminase, fused to nCas9, gains access to the exposed strand and converts cytosine to uracil within an editing window; uridine is subsequently transformed into thymidine during DNA replication. The uracil DNA glycosylase inhibitor (UGI) prevents repair of the deaminated cytidine by the endogenous DNA repair machinery. PAM, protospacer adjacent motif. B Deamination of a cytidine residue subsequently leads to uridine and thymidine. C In silico genome analysis of open reading frames (ORFs) annotated in P. putida KT2440 and D P. aeruginosa PA14 reveals the scope of base editing across the bacterial chromosomes. The CBE can be used to interrupt ca. 92 and 75% of all ORFs in P. putida and P. aeruginosa PA14, respectively, by introducing STOP codons at the positions indicated. Source data underlying panels C, D are provided as a Source Data file.