Programmable protein editing by split intein-mediated recombination

Abstract Biological regulation has long relied on modifying genes, transcripts, or protein abundance, yet direct rewriting of protein sequence after translation remains largely inaccessible. Here, we introduce a programmable protein editing platform based on split intein-mediated recombination, enabling precise excision and replacement of defined segments within mature proteins in living cells. By covalently exchanging a target segment with a donor-encoded sequence supplied in trans, this approach functions as a protein-level analogue of recombination, operating independently of transcription or translation. Using ultrafast and orthogonal split inteins, we demonstrate efficient protein recombination in mammalian cells, enabling single-amino acid substitutions, domain replacement, functional switching, and reprogramming of subcellular localization. This work establishes post-translational protein recombination as a general strategy for sequence-level control of protein function, expanding the conceptual and practical scope of biological editing beyond nucleic acids.