Site-specific protein cleavage in vivo by an intein-derived protease

Site-specific protein cleavage is a ubiquitous process in cellular protein metabolism, yet molecular tools to provide control of protein cleavage inside living cells remain scarce. Here, we show that the C-terminal intein fragment of the non-canonical Ssp (Synechocystis sp. PCC6803) DnaB S1 split-intein can be used as a site-specific protease for in vivo protein cleavage both in bacterial and eukaryotic cells. Mutagenesis data indicate a broad tolerance of the intein-derived protease (IP) toward the amino acid upstream of the cleavage site. Furthermore, deletion studies reveal that the recognition sequence for the IP can be as short as ten amino acids. The structural features underlying the cleavage reaction preclude unintended proteolysis of endogenous proteins, thus ensuring that negative effects on cell viability are minimal.

► An intein-derived protease can catalyze protein cleavage in vivo.
► The recognition sequence for the protease can be as short as ten amino acids.
► Any amino acid can be upstream of the cleavage site.
► The reaction proceeds in both prokaryotic and eukaryotic cells.
► No negative effects on cell viability have been observed.