Engineering Compact Base Editors by AlphaFold-Guided Mutation Scan and Escherichia coli-Based Tri-Selection

APOBEC1-based cytosine base editors such as BE4max enable base conversion, but many alternative deaminases show low activity and cytotoxicity, especially when miniaturized for delivery. SsdA_tox, a DNA deaminase toxin from Pseudomonas syringae that is two-thirds the size of APOBEC1, is attractive for compact base editors but, in native form, shows low C-to-T editing efficiency and high cytotoxicity. Guided by an AlphaFold- and CASTpFold-based alanine scan, we identified K31 as a gatekeeping residue whose substitution enlarges the modeled DNA binding pocket. Site-saturation mutagenesis at K31 produced variants with ten-fold higher activity but increased indel formation. To further enhance activity while reducing indels and cytotoxicity, we developed Trinity-Screen, an Escherichia coli (E. coli)-based three-in-one directed evolution platform that selects for high activity and reduced double-strand break-associated indels. Trinity-Screen revealed four additional DNA-binding positions; combinatorial mutagenesis at these sites generated four- and five-site SsdA_tox variants that retained high activity yet showed lower indel rates and rescued bacterial viability. To standardize comparisons, we defined the Base Editor Performance Index (BEPI), which integrates C-to-T conversion and indel frequency. Optimized SsdA_tox variants achieved up to 31-fold improvement relative to wild type, outperforming BE4max at multiple endogenous targets and displaying ten-fold lower cytotoxicity in E. coli.