Affinage

PREPL

Prolyl endopeptidase-like · UniProt Q4J6C6

Length
727 aa
Mass
83.9 kDa
Annotated
2026-06-10
20 papers in source corpus 9 papers cited in narrative 9 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 4/5 claims corpus-supported (80%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

PREPL is a cytosolic serine hydrolase of the prolyl oligopeptidase family that performs two genetically separable functions—an enzymatic activity required for normal mitochondrial respiration and a non-enzymatic role as an effector of the AP-1 clathrin adaptor complex (PMID:39078710). Its catalytic machinery comprises a serine hydrolase triad (Ser470, Asp556, His601) localized to the C-terminal domain; mutation of these residues abolishes labeling by serine hydrolase-directed probes, and recombinant PREPL reacts with active-site inhibitors and slowly hydrolyzes activated esters yet fails to cleave peptides bearing a P1 basic residue, defining it as an esterase with negligible canonical peptidase activity (PMID:16385448, PMID:16143824). The non-enzymatic function arises through direct binding to the N-terminus of the AP-1 μ1A subunit, where PREPL regulates AP-1 membrane cycling: it limits AP-1 membrane association and is required for AP-1 recycling, and its loss expands the trans-Golgi network in patient cells, a defect rescued by PREPL re-expression (PMID:23321636). Catalytically dead PREPL (Ser559Ala) retains normal AP-1-mediated TGN transport while failing to support mitochondrial function, and CMS22 patient missense variants disrupt interactor binding rather than hydrolase activity, cementing the division between the two roles (PMID:39078710). Loss of PREPL causes triacylglycerol and lipid-droplet accumulation as a secondary consequence of mitochondrial dysfunction rather than a direct lipase activity [PMID:bio_10.1101_2025.10.28.685080]. PREPL deficiency causes a congenital myasthenic syndrome with combined pre- and postsynaptic neuromuscular transmission defects, and PREPL-null mice show reduced growth and neonatal hypotonia (PMID:24610330, PMID:24586561).

Mechanistic history

Synthesis pass · year-by-year structured walk · 7 steps
  1. 2005 High

    Established that PREPL is a genuine but atypical serine hydrolase, resolving whether its predicted prolyl-oligopeptidase-family triad is catalytically functional.

    Evidence Activity-based probe labeling with catalytic-residue alanine mutagenesis and subcellular fractionation; recombinant protein with DSC, inhibitor labeling, and peptide/ester substrate assays

    PMID:16143824 PMID:16385448

    Open questions at the time
    • No physiological substrate of the esterase activity identified
    • Biological consequence of catalysis not connected to a cellular process at this stage
  2. 2009 Medium

    Defined the transcriptional control of PREPL, showing it shares a bidirectional GC-rich promoter with C2ORF34 driven cooperatively by NRF-2 and YY-1.

    Evidence Promoter deletion/reporter assays and transcription factor binding analysis across tissues

    PMID:19575798

    Open questions at the time
    • Does not link transcriptional regulation to a specific physiological stimulus
    • Tissue-specific repressive elements not mapped to defined factors
  3. 2011 Medium

    Demonstrated PREPL is a druggable functional serine hydrolase in cells and in vivo, providing tools to probe its enzymatic role.

    Evidence Fluopol-ABPP high-throughput screen (~300,000 compounds), cell-based activity assay, and mouse pharmacokinetics

    PMID:21692504

    Open questions at the time
    • Inhibitor phenotype on cellular function not assessed
    • No endogenous substrate revealed by inhibition
  4. 2013 High

    Identified the first defined cellular function of PREPL as a non-enzymatic AP-1 effector controlling adaptor membrane cycling and TGN morphology.

    Evidence Yeast two-hybrid screen against μ1A, AP-1 membrane binding assays, overexpression/knockdown, and patient cell line complementation

    PMID:23321636

    Open questions at the time
    • Whether the interaction depends on catalytic activity not tested here
    • Mechanism by which PREPL displaces AP-1 from membranes unresolved
  5. 2014 Medium

    Connected PREPL loss to neuromuscular disease, showing combined pre- and postsynaptic transmission defects and an organismal growth/tone phenotype.

    Evidence Neuromuscular electrophysiology in patient tissue with immunoblot/histochemistry; exon-11-deletion PREPL knockout mouse with body measurements and righting reflex assay

    PMID:24586561 PMID:24610330

    Open questions at the time
    • Molecular cause of the synaptic defect inferred from AP-1 interaction rather than directly demonstrated
    • Mouse phenotype not mechanistically tied to AP-1 versus enzymatic function
  6. 2024 High

    Dissected PREPL's two activities, proving hydrolase function is required for mitochondrial function but dispensable for AP-1-mediated TGN transport, and that disease variants act by disrupting interactions.

    Evidence CRISPR catalytic-dead (Ser559Ala) knock-in cell lines, mitochondrial and AP-1 transport assays, hydrolase activity assays, structural analysis, and interaction studies of CMS22 variants

    PMID:39078710

    Open questions at the time
    • Substrate and molecular mechanism linking PREPL catalysis to mitochondrial respiration unknown
    • Specific interactors lost by CMS22 variants not fully enumerated
  7. 2025 Medium

    Clarified the lipid phenotype of PREPL loss, arguing against a direct lipase role and attributing triacylglycerol and peroxisome changes to secondary mitochondrial dysfunction.

    Evidence Unbiased lipidomics in KO mouse brain and CRISPR KO cells, lipid droplet imaging, peroxisome morphology/protein analysis, and localization studies (preprint)

    PMID:bio_10.1101_2025.10.28.685080

    Open questions at the time
    • Preprint not yet peer-reviewed
    • Direct biochemical link between PREPL catalysis and fatty acid β-oxidation not established

Open questions

Synthesis pass · forward-looking unresolved questions
  • The endogenous physiological substrate of PREPL's esterase activity and the molecular mechanism coupling that activity to mitochondrial respiration remain unidentified.
  • No in vivo substrate identified despite confirmed esterase activity
  • Mechanism by which PREPL binding regulates AP-1 membrane release is undefined
  • Causal chain from catalytic loss to mitochondrial dysfunction not reconstituted

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0016787 hydrolase activity 4 GO:0060090 molecular adaptor activity 1
Localization
GO:0005829 cytosol 2 GO:0005794 Golgi apparatus 1
Pathway
R-HSA-1430728 Metabolism 2 R-HSA-5653656 Vesicle-mediated transport 1
Partners

Evidence

Reading pass · 9 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2005 PREPL is localized in the cytosol and possesses a catalytic triad (Ser470, Asp556, His601); substitution of these predicted catalytic residues by alanines resulted in loss of reactivity with a serine hydrolase-specific activity-based probe, confirming an intact but unique catalytic machinery. Unlike prolyl oligopeptidase and oligopeptidase B, PREPL activity depends only on the carboxyterminal domain. Activity-based probe labeling with catalytic-residue alanine mutagenesis; subcellular fractionation American journal of human genetics High 16385448
2005 PREPL A (638-residue splice variant) was purified from E. coli and shown to have secondary structure similar to oligopeptidase B; it reacted with diisopropyl fluorophosphate and slowly hydrolyzed an activated ester substrate, confirming a reactive catalytic serine. However, PREPL A did not cleave peptide substrates with a P1 basic residue (Arg/Lys), indicating negligible canonical peptidase activity and suggesting a non-peptidase biological function. Dimerization was observed and may account for enhanced conformational stability. Recombinant protein expression and purification, differential-scanning calorimetry, enzyme activity assays with peptide and activated ester substrates, DFP inhibitor labeling Cellular and molecular life sciences : CMLS High 16143824
2013 PREPL (cytoplasmic) was identified as a direct interaction partner of the N-terminal 70 amino acids of AP-1 complex subunit μ1A via yeast two-hybrid screen. PREPL overexpression reduced AP-1 membrane binding, while reduced PREPL expression increased AP-1 membrane binding and impaired AP-1 recycling. PREPL-deficient patient cell lines displayed an expanded trans-Golgi network that was rescued by PREPL re-expression. PREPL colocalizes with residual membrane-bound AP-1, functioning as an AP-1 effector regulating AP-1 membrane association and TGN morphology. Yeast two-hybrid screen; AP-1 membrane binding assays; PREPL overexpression and knockdown; colocalization by fluorescence microscopy; patient cell line complementation Journal of cell science High 23321636
2014 PREPL deficiency causes a congenital myasthenic syndrome with decreased quantal content of the endplate potential and reduced miniature endplate potential amplitude without acetylcholine receptor deficiency or altered endplate geometry, indicating both pre- and postsynaptic defects. The myasthenia is attributed to abrogated PREPL interaction with adaptor protein 1 (AP-1). No PREPL expression was detected in patient muscle and endplates. Electrophysiology (in vitro neuromuscular transmission studies), immunoblot, histochemistry, ultrastructural studies in patient with isolated PREPL deficiency Neurology Medium 24610330
2014 Deletion of exon 11 from the mouse Prepl gene (which encodes key catalytic amino acids) leads to loss of PREPL protein and reduced Prepl mRNA. PREPL-null mice exhibit significantly reduced growth (shorter and lighter) and neonatal hypotonia as measured by a righting reflex assay, establishing that PREPL is required for normal growth and neonatal muscle tone in vivo. PREPL knockout mouse model (exon 11 deletion); body measurement; righting assay for neonatal hypotonia PloS one Medium 24586561
2011 A fluorescence polarization activity-based protein profiling (fluopol-ABPP) screen identified selective small-molecule inhibitors of PREPL serine hydrolase activity that block PREPL activity in cells. One inhibitor (1-isobutyl-3-oxo-3,5,6,7-tetrahydro-2H-cyclopenta[c]pyridine-4-carbonitrile) distributed to the brain after administration to mice, confirming PREPL is a functional serine hydrolase amenable to pharmacological inhibition. Fluopol-ABPP high-throughput screen (~300,000 compounds); cell-based activity assay; mouse pharmacokinetics Journal of the American Chemical Society Medium 21692504
2009 NRF-2 and YY-1 transcription factors cooperatively bind a 243-bp GC-rich bidirectional minimal promoter within the 405-bp intergenic region between PREPL and C2ORF34, driving expression of both genes in an additive manner. Cis-acting repressive elements within this region also contribute to tissue-specific expression. Promoter deletion/reporter assays, transcription factor binding studies (gel shift/ChIP implied), expression analysis across tissues BMC molecular biology Medium 19575798
2024 Missense variants in PREPL from CMS22 patients do not impair hydrolase activity but reduce binding to known interactors, and structural analysis indicates the variants affect regions involved in intraprotein or protein-protein interactions. Catalytically inactive PREPL p.Ser559Ala cell lines showed that hydrolytic activity of PREPL is required for normal mitochondrial function but NOT for regulating AP-1-mediated transport in the trans-Golgi network, demonstrating that PREPL has separable enzymatic and non-enzymatic functions. Biochemical hydrolase activity assays; structural analysis; protein-protein interaction assays; CRISPR catalytic-dead knock-in (Ser559Ala) cell lines; mitochondrial function assays; AP-1 transport assays JCI insight High 39078710
2025 In PREPL KO HEK293T cells and Prepl KO mouse brains, global phospholipid composition was largely unchanged, arguing against a direct lipase role for PREPL in (lyso)phospholipid turnover. However, PREPL KO cells accumulated triacylglycerols (TAGs) and increased lipid droplets. PREPL does not localize to peroxisomes, and peroxisome numbers and protein levels were largely unaffected, but KO cells showed elongated peroxisomes. The TAG accumulation and peroxisome elongation are interpreted as secondary consequences of mitochondrial dysfunction (impaired fatty acid β-oxidation) caused by PREPL loss, not a direct lipase function. Unbiased lipidomics in KO mouse brain and CRISPR-Cas9 KO cell lines; lipid droplet imaging; peroxisome morphology and protein level analysis; PREPL localization studies bioRxivpreprint Medium bio_10.1101_2025.10.28.685080

Source papers

Stage 0 corpus · 20 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2005 Deletion of PREPL, a gene encoding a putative serine oligopeptidase, in patients with hypotonia-cystinuria syndrome. American journal of human genetics 69 16385448
2014 PREPL deficiency with or without cystinuria causes a novel myasthenic syndrome. Neurology 48 24610330
2008 Deletion of C2orf34, PREPL and SLC3A1 causes atypical hypotonia-cystinuria syndrome. Journal of medical genetics 37 18234729
2006 PREPL: a putative novel oligopeptidase propelled into the limelight. Biological chemistry 30 16913837
2005 The PREPL A protein, a new member of the prolyl oligopeptidase family, lacking catalytic activity. Cellular and molecular life sciences : CMLS 29 16143824
2017 PREPL deficiency: delineation of the phenotype and development of a functional blood assay. Genetics in medicine : official journal of the American College of Medical Genetics 28 28726805
2011 A substrate-free activity-based protein profiling screen for the discovery of selective PREPL inhibitors. Journal of the American Chemical Society 23 21692504
2013 Trans-Golgi network morphology and sorting is regulated by prolyl-oligopeptidase-like protein PREPL and the AP-1 complex subunit μ1A. Journal of cell science 22 23321636
2011 PREPL, a prolyl endopeptidase-like enzyme by name only?--Lessons from patients. CNS & neurological disorders drug targets 19 21222627
2014 Deletion of PREPl causes growth impairment and hypotonia in mice. PloS one 17 24586561
2009 Cooperation between NRF-2 and YY-1 transcription factors is essential for triggering the expression of the PREPL-C2ORF34 bidirectional gene pair. BMC molecular biology 14 19575798
2020 PREPL Deficiency: A Homozygous Splice Site PREPL Mutation in a Patient With Congenital Myasthenic Syndrome and Absence of Ovaries and Hypoplasia of Uterus. Frontiers in genetics 11 32218803
2018 The second point mutation in PREPL: a case report and literature review. Journal of human genetics 11 29483676
2009 Deletion of C2orf34, PREPL and SLC3A1 causes atypical hypotonia-cystinuria syndrome. BMJ case reports 9 21686663
2020 First maternal uniparental disomy for chromosome 2 with PREPL novel frameshift mutation of congenital myasthenic syndrome 22 in an infant. Molecular genetics & genomic medicine 8 31985178
2021 Cleavage of PrePL by Lon promotes growth and pathogenesis in Magnaporthe oryzae. Environmental microbiology 7 33225564
2024 Missense variants in CMS22 patients reveal that PREPL has both enzymatic and nonenzymatic functions. JCI insight 2 39078710
2025 Uncovering the mechanism of Buyang Huanwu Decoction in regulating mitochondrial dysfunction to alleviate atherosclerosis: BTK, PREPL, and P2RX7 proteins play key roles. International journal of biological macromolecules 1 40494461
1991 Semianalytical expressions for (L/rho)(air)med and P(repl) for electron beams. Medical physics 1 1908048
1995 Proposed semi-analytical formulae for the determination of (L/rho)medair and Prepl for electron beams as used in radiotherapy. Medical dosimetry : official journal of the American Association of Medical Dosimetrists 0 7632347

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