The first challenge in construction of a new protease-based signaling cascade was the selection of appropriate proteases. The candidate proteases should: i) recognize defined target cleavage sequences, preferably as long as possible; ii) be active in mammalian cells, but not toxic to them and iii) be inducible, ideally through the reconstitution of split protein fragments. Most importantly, a large number of proteases with similar properties but different substrates should be available to allow for modular construction of signaling pathways and logic functions. These proteases should be orthogonal to each other, meaning that their specific cleavage sites should not be recognized by other proteases in the system.
We found that the tobacco etch virus protease (TEVp) was the only protease described in the literature to match our criteria.
TEV protease is a highly specific, 242 amino acids long, 27 kDa cysteine
protease, that originates from the tobacco etch virus (TEV) of the Potyvirus
It has a target recognition sequence of seven amino acids, ENLYFQ-S/G, where
cleavage occurs after the glutamine residue (denoted by the – symbol),
and the final residue of the recognition sequence can be either S or G (denoted
by the / symbol). This substrate sequence is scarcely represented in the
proteome. TEV protease is therefore relatively non-toxic
Despite its widespread use in biotechnology, TEVp also displays some
shortcomings, the most prominent of them being self-cleavage. Substitution
of Ser-219 with Val or Pro
To overcome the lack of inducible orthogonal proteases, we looked for the characterized TEVp mutants and naturally occurring proteases, closely related to TEVp that might also be used to function as split proteases.
Based on the sequence alterations described by Yi et al.
Yi et al.
To test these two proteases we used a cleavable firefly luciferase (fLuc) reporter with an appropriate cleavage sequence inserted in a permissible site. We observed a significant decrease in luciferase activity upon co-expression of the reporters and their corresponding proteases, whereas co-expression of an orthogonal protease did not decrease the luciferase activity (1). These results were additionally confirmed by results from western blotting, where cleavage of the luciferase reporter was detected only in the presence of the corresponding protease, but not in the presence of orthogonal proteases (2).
No data has previously been reported on TEVpE and TEVpH toxicity, therefore we expressed each TEVp variant in HEK293T cells and performed a viability assay. Even after transfection with a high amount of the plasmid for each respective protease, the cells showed high viability, with practically no difference when compared to cells transfected with a mock plasmid (3).
Introduction of two new TEVp variants expanded our repertoire of tools, demonstrating that we can use the results of mutational screenings for protease variants. However, a larger number of strictly orthogonal proteases would be required for modular design of complex logic circuits. We therefore decided to investigate the activity of de novo created split proteases from the potyviridae family.
The NIa proteases from the potyviridae group of plant viruses in general
recognize a seven amino acid sequence motif as their substrate. They are
are classified as cysteine proteases with an active site closely related to
eukaryotic serine proteases. The NIa proteases adopt a characteristic
two-domain antiparallel β-barrel fold. The active site of the protease
comprises a catalytic triad: His-46, Asp-81, Cys-151 (amino acids numbered
according to the TEVp sequence) with a Gly-x-Cys-Gly motif around the active
We searched for different potyviruses available on UniProt (4), paying particular attention to any evidence of orthogonality among their target substrates. We decided to test the plum pox virus protease (PPVp), the soybean mosaic virus protease (SbMVp), and the sunflower mild mosaic virus protease (SuMMVp).
PPVp is one of the most studied potyviral proteases after the TEV protease.
Its substrate (PPVs) has an amino acid sequence NVVVHQ-A.
In contrast to TEVp, it has been reported that PPVp is resistant to
self-cleavage at the C-terminus
SbMVp has been recently studied by Seo et al. as a tool for protein-protein interaction studies in the soybean plant. The substrate (SbMVs) has been determined to be the sequence ESVSLQ-S
Similarly, SuMMVp has been used by Fernandez-Rodriguez et al.
All selected potyviral proteases were designed as synthetic genes and their activity was tested in mammalian cells using cyclic luciferase reporters, which propagate luciferase activity only upon cleavage. We detected an increase of luciferase activity only in the corresponding protease-reporter pairs, confirming exquisite orthogonality of the selected proteases and their activity in the human cell chassis (5).