One-for-all gene inactivation via PAM-independent base editing in bacteria

Base editing is preferable for bacterial gene inactivation without generating double-strand breaks, requiring homology recombination, or highly efficient DNA delivery capability. However, the potential of base editing is limited by the adjoined dependence on the editing window and protospacer adjacent motif. Herein, we report an unconstrained base-editing system to enable the inactivation of any genes of interest in bacteria. We employed a dCas9 derivative, dSpRY, and activation-induced cytidine deaminase to build a protospacer adjacent motif-independent base editor. Then, we programmed the base editor to exclude the START codon of a gene of interest instead of introducing premature STOP codons to obtain a universal approach for gene inactivation, namely XSTART, with an overall efficiency approaching 100%. By using XSTART, we successfully manipulated the amino acid metabolisms in Escherichia coli, generating glutamine, arginine, and aspartate auxotrophic strains. While we observed a high frequency of off-target events as a trade-off for increased efficiency, refining the regulatory system of XSTART to limit expression levels reduced off-target events by over 60% without sacrificing efficiency, aligning our results with previously reported levels. Finally, the effectiveness of XSTART was also demonstrated in probiotic E. coli Nissle 1917 and photoautotrophic cyanobacterium Synechococcus elongatus, illustrating its potential in reprogramming diverse bacteria.