Open Access

Members of the Signal Peptide-Peptidase (SPP) and Signal Peptide-Peptidase-like (SPPL) family are intramembrane aspartyl-proteases like their well-studied homologs, the presenilins, which comprise the catalytically active subunit within the γ-secretase complex. The lack of in vitro cleavage assays for SPPL proteases limited their biochemical characterization as well as substrate identification and validation. So far, SPPL proteases have been analyzed exclusively in intact cells or membranes, restricting mechanistic analysis to co-expression of enzyme and substrate variants colocalizing in the same subcellular compartments. We describe the details of developing an in vitro cleavage assay for SPPL2b and its model substrate TNFα and analyzed the influence of phospholipids, detergent supplements, and cholesterol on the SPPL2b in vitro activity. SPPL2b in vitro activity resembles mechanistic principles that have been observed in a cellular context, such as cleavage sites and consecutive turnover of the TNFα transmembrane domain. The novel in vitro cleavage assay is functional with separately isolated protease and substrate and amenable to a high throughput plate-based readout overcoming previous limitations and providing the basis for studying enzyme kinetics, catalytic activity, substrate recognition, and the characteristics of small molecule inhibitors. As a proof of concept, we present the first biochemical in vitro characterization of the SPPL2a and SPPL2b specific small molecule inhibitor SPL-707.

The C-terminal domain (CTD) of RNA polymerase II (Pol II) integrates nuclear events by binding proteins involved in mRNA biogenesis. CTD-binding proteins recognize a specific CTD phosphorylation pattern, which changes during the transcription cycle, due to the action of CTD-modifying enzymes. Structural and functional studies of CTD-binding and -modifying proteins now reveal some of the mechanisms underlying CTD function. Proteins recognize CTD phosphorylation patterns either directly, by contacting phosphorylated residues, or indirectly, without contact to the phosphate. The catalytic mechanisms of CTD kinases and phosphatases are known, but the basis for CTD specificity of these enzymes remains to be understood.

Signal peptide peptidase-like (SPPL) proteases, members of the intramembrane aspartyl protease family, have attracted increased interest due to their involvement in immune cell differentiation and cellular glycan structure regulation. However, the enzymatic domain involved in substrate recognition remains enigmatic. Here we provide evidence that the N-terminal protease-associated (PA) domains of the SPPL2 subfamily are involved in substrate recognition and discrimination of substrates that differ slightly in their luminal/extracellular domain. Presence of the SPPL2c PA domain impairs SPPL2a/b mediated tumor necrosis factor α (TNFα) initial cleavage, kinetics, and processivity in cells and in vitro. In contrast, the SPPL2a PA domain enhances processing by SPPL2b. Additionally, we demonstrate non-canonical shedding activity of SPPL3 on full-length TNFα and that the ability for consecutive cleavage differs within the SPPL-family and is mainly based on the SPPL2a/b membrane spanning body. This provides the basis to finally understand the mechanistic differences of these homologous proteases.