PPIL1

PPIL1 is a spliceosomal cyclophilin-family peptidyl-prolyl cis/trans isomerase that supports pre-mRNA splicing fidelity, particularly of short, GC-rich introns, through a structural rather than enzymatic role within the activated spliceosome. It is recruited to the spliceosome via a direct, cyclosporin A-independent interaction between a site distinct from its PPIase active site and the intrinsically disordered N-terminal region (residues 59–79) of SKIP/SNW1, while its catalytic face engages PRP17 in an isomerase–substrate complex whose prolyl isomerase activity is dispensable for splicing function (PMID:16595688, PMID:20007319, PMID:33220177). Biallelic loss-of-function mutations in PPIL1 cause pontocerebellar hypoplasia with microcephaly through neuron-specific apoptosis in humans and mice (PMID:33220177). Beyond splicing, PPIL1 participates in C3b-mediated NLRP3 inflammasome activation via residues E156 and D111 (PMID:36476873), modulates EWS low-complexity domain phase separation through PPIase active-site contacts with PxxP motifs (PMID:40668764), and promotes Wnt/β-catenin signaling through transcriptional upregulation of DAAM2 in hepatocellular carcinoma (PMID:40883023).

1. 1996 Medium

   Identification of PPIL1 as a novel cyclophilin-family member established that a short (166 aa) PPIase-related protein exists in the human genome at 2p23, opening questions about its specific substrates and cellular role.

   Evidence cDNA cloning, Northern blot, and FISH mapping of hCyPX

   PMID:8978786

   Open questions at the time

   • No enzymatic activity demonstrated
   • No interacting partners or cellular function identified
2. 2001 Medium

   Discovery that PPIL1 orthologs bind the SNW/SKIP coregulator in a cyclosporin A-independent manner while retaining CsA-sensitive PPIase activity revealed a bipartite functionality—enzyme activity and a distinct protein-recruitment interface—and placed PPIL1 in the spliceosomal/transcriptional regulatory axis.

   Evidence Yeast two-hybrid screen and in vitro PPIase assay in Dictyostelium and S. pombe systems

   PMID:11690648

   Open questions at the time

   • Binding interface not mapped at residue level
   • Human PPIL1–SKIP interaction not yet directly demonstrated
3. 2006 High

   Structural and biophysical characterization defined two separable surfaces on PPIL1—a PPIase active site and a distinct SKIP-binding face—with nanomolar affinity for SKIP residues 59–129, establishing how PPIL1 can simultaneously bind SKIP and present its catalytic pocket to spliceosomal substrates.

   Evidence NMR structure, SPR (Kd = 1.25 × 10⁻⁷ M), GST pulldown, chemical shift perturbation; X-ray crystallography at 1.15 Å resolution with peptide array and docking

   PMID:16595688 PMID:20368803

   Open questions at the time

   • Identity of the PPIase substrate in the spliceosome unknown
   • Functional significance of isomerase activity untested
4. 2009 High

   Demonstration that the SKIP N-terminus is intrinsically disordered and undergoes a disorder-to-order transition upon binding PPIL1, with a minimal 21-residue fragment sufficient, clarified the recruitment mechanism and showed the PPIase active site remains accessible for additional substrates.

   Evidence NMR structure of PBF·PPIL1 complex and disorder characterization

   PMID:20007319

   Open questions at the time

   • In vivo relevance of disorder-to-order transition not tested
   • No spliceosomal substrate for the free active site identified
5. 2020 High

   Human genetics and mouse modeling resolved the key outstanding questions: PPIL1 forms an isomerase–substrate complex with PRP17, but its PPIase catalytic activity is dispensable; loss of PPIL1 disrupts splicing of short, GC-rich introns and causes neuron-specific apoptosis leading to pontocerebellar hypoplasia with microcephaly.

   Evidence WES of 10 families with PCHM, knockin and knockout mouse models, transcriptome-wide splicing analysis, biochemical interaction assays

   PMID:33220177

   Open questions at the time

   • Structural basis for the non-enzymatic PRP17 interaction unresolved
   • Why neurons are selectively vulnerable unclear
   • Whether PPIL1 has additional spliceosomal substrates beyond PRP17 unknown
6. 2022 Medium

   Identification of PPIL1 as a C3b-α'2 interactor through E156 and D111 residues revealed a non-spliceosomal role in NLRP3 inflammasome activation and tumor metastasis, broadening PPIL1's functional repertoire to innate immunity.

   Evidence Inactivating mutations, co-immunoprecipitation, mouse lung colonization assays

   PMID:36476873

   Open questions at the time

   • Whether PPIase activity is required for C3b interaction not tested
   • How PPIL1–C3b interaction triggers inflammasome assembly mechanistically unclear
   • Single-lab finding
7. 2025 Medium

   Two independent studies extended PPIL1's non-spliceosomal roles: its PPIase active site engages EWS low-complexity domain PxxP motifs in fuzzy complexes that modulate phase separation, and it promotes Wnt/β-catenin signaling via DAAM2 upregulation in hepatocellular carcinoma.

   Evidence NMR titration and phase separation assays (EWS); shRNA knockdown, xenograft models, and transcriptome analysis (HCC/DAAM2)

   PMID:40668764 PMID:40883023

   Open questions at the time

   • Physiological relevance of PPIL1–EWS condensate modulation untested in cells
   • Whether PPIL1-DAAM2 axis operates through direct interaction or is transcriptionally indirect not resolved
   • Relationship between spliceosomal and phase-separation roles unclear

• The structural basis for PPIL1's non-enzymatic stabilization of PRP17 within the spliceosome, the mechanism of neuron-selective vulnerability to PPIL1 loss, and the functional integration of its spliceosomal versus non-spliceosomal roles remain unresolved.
• No high-resolution structure of PPIL1–PRP17 complex available
• Neuron-specific splicing dependencies of PPIL1 not mapped
• Whether spliceosomal and inflammasome/phase-separation functions are coordinated or independent is unknown