PLEKHM1

PLEKHM1 is a multivalent endolysosomal adaptor that coordinates the convergence of endocytic and autophagic cargo on the lysosome by simultaneously engaging active RAB7, the HOPS tethering complex, and LC3/GABARAP-decorated autophagosomal membranes (PMID:25498145). It binds GTP-bound RAB7 directly through a C-terminal Rubicon-homology (RH) domain, an interaction required for its control of endocytic transport (PMID:20943950), and a conserved LC3-interacting region (LIR) couples this RAB7/HOPS platform to autophagosomal membranes so that PLEKHM1 drives lysosomal degradation of endocytic cargo such as EGFR, autophagic flux, and clearance of protein aggregates (PMID:25498145). Its recruitment to late endosomes is dynamically switched by a PI4P-to-PI(4,5)P2 lipid conversion cycle that drives RAB7 inactivation and releases PLEKHM1 from the membrane (PMID:31368593). In osteoclasts, PLEKHM1 forms a positioning machinery with DEF8 (which promotes its RAB7 binding), FAM98A, and NDEL1 to distribute lysosomes peripherally and link them to microtubules, enabling ruffled-border formation and bone resorption (PMID:27777970); loss-of-function mutations in PLEKHM1 cause osteopetrosis through failure of osteoclast ruffled-border formation and defective bone resorption (PMID:17404618). The pathway is exploited by the Salmonella effector SifA, which binds the PLEKHM1 PH2 domain to redirect phagolysosomal membranes to the Salmonella-containing vacuole (PMID:25500191), and excess PLEKHM1 itself disrupts late-stage autophagy in vivo, impairing autolysosome maturation and cargo degradation in neurons (PMID:40940751).

1. 2007 High

   Established PLEKHM1 as an essential factor in osteoclast vesicular transport by showing its RAB7-dependent localization to late endosomal/lysosomal membranes and the failure of ruffled-border formation when it is mutated.

   Evidence Confocal and electron microscopy with mutational analysis in patient osteoclasts and HEK293 cells

   PMID:17404618

   Open questions at the time

   • Did not define the molecular domain mediating RAB7 association
   • Mechanism linking RAB7 colocalization to ruffled-border formation unresolved
2. 2008 Medium

   Connected a disease mutation to organelle function by showing the R714C variant impairs endosomal acidification and increases TRACP secretion in osteoclasts.

   Evidence Transfection of wild-type vs R714C mutant in HEK293 and RAW 264.7 cells with endosomal pH and TRACP activity assays

   PMID:17997709

   Open questions at the time

   • Did not show how the mutation mechanistically disrupts acidification
   • Single lab; R714C effect on RAB7 binding not tested
3. 2010 High

   Identified the molecular basis of RAB7 engagement by mapping the interaction to a C-terminal Rubicon-homology domain and distinguishing PLEKHM1 from Rubicon in not binding PI3-kinase.

   Evidence Homology searches, direct binding assays, and functional knockdown of endocytic transport

   PMID:20943950

   Open questions at the time

   • Autophagy role explicitly excluded here but later revised
   • No structural model of the RH-RAB7 interface
4. 2014 High

   Defined PLEKHM1 as a tripartite adaptor bridging endocytic and autophagy pathways by demonstrating simultaneous binding to RAB7, HOPS, and LC3/GABARAP via a LIR motif, with functional control of EGFR degradation, autophagy flux, and aggregate clearance.

   Evidence GTP-RAB7 pulldown mass spectrometry, yeast two-hybrid LIR screen, knockout MEFs, and degradation/clearance assays

   PMID:25498145

   Open questions at the time

   • Did not address how membrane recruitment is temporally regulated
   • Stoichiometry of the RAB7-HOPS-LC3 complex unresolved
5. 2014 High

   Revealed pathogen hijacking of the adaptor by showing the Salmonella effector SifA binds the PLEKHM1 PH2 domain to redirect phagolysosomal membranes to the bacterial vacuole.

   Evidence Direct SifA-PH2 binding assays, siRNA knockdown, and infection assays in cells and mice

   PMID:25500191

   Open questions at the time

   • Did not resolve how SifA binding alters native PLEKHM1-RAB7-HOPS function
   • Endogenous ligand of the PH2 domain unknown
6. 2015 Medium

   Added TRAFD1 as a pathway component by mapping its zinc-finger to a PLEKHM1 region between the PH2 and C1 domains and showing its loss blocks osteoclast resorption and acidification.

   Evidence Mass spectrometry, deletion-based domain mapping, and stable shRNA knockdown with acidification/resorption readouts

   PMID:25992615

   Open questions at the time

   • Functional consequence of the TRAFD1-PLEKHM1 interaction at the molecular level unclear
   • Single lab; not validated in other systems
7. 2016 High

   Built the osteoclast lysosome-positioning machine by showing DEF8 promotes PLEKHM1-RAB7 binding and FAM98A/NDEL1 link lysosomes to microtubules, with KO mice displaying increased bone mass and defective lysosome trafficking.

   Evidence Germline and conditional KO mice, co-immunoprecipitation, lysosome positioning and bone resorption assays, and siRNA of partners

   PMID:27777970

   Open questions at the time

   • Architecture of the DEF8-FAM98A-NDEL1-PLEKHM1 assembly not structurally defined
   • How microtubule coupling is regulated unresolved
8. 2016 Medium

   Linked a disease deletion to mechanism by showing an exon 11 frameshift impairing the RH domain reduces PLEKHM1-RAB7 binding and disrupts EGFR degradation and LC3 conversion.

   Evidence Co-immunoprecipitation, EGFR degradation and LC3-I/II ratio assays in HEK293 and U937 cells

   PMID:27291868

   Open questions at the time

   • Single lab; physiological phenotype not assessed in patient tissue
   • Does not distinguish endocytic from autophagic contributions
9. 2019 High

   Established dynamic regulation of PLEKHM1 membrane association by showing a PI4P-to-PI(4,5)P2 conversion drives RAB7 dissociation and PLEKHM1 release, with PI4K2A loss impairing RAB7 inactivation and autophagosome-lysosome fusion.

   Evidence Chemogenetic acute lipid conversion, PI4K2A deletion, live imaging, and RAB7 dissociation assays

   PMID:31368593

   Open questions at the time

   • Did not define the kinases/phosphatases acting upstream in physiological signaling
   • Whether PLEKHM1 directly senses lipids vs follows RAB7 unresolved
10. 2023 Medium

    Identified a scaffolding regulator of fusion by showing TRIM22 bridges GABARAP proteins to PLEKHM1 independent of its E3 ligase activity to promote autophagic aggregate clearance.

    Evidence Co-immunoprecipitation, proximity ligation, TRIM22 knockout/rescue, and a ligase-dead mutant

    PMID:38009729

    Open questions at the time

    • Single lab; structural basis of the TRIM22-PLEKHM1-GABARAP assembly unknown
    • Physiological contexts requiring TRIM22 vs LIR-direct binding undefined
11. 2024 Medium

    Dissected the RH domain functionally by structure-guided mutagenesis, separating residues required for protein stability from those required for RAB7 binding, both impairing lysosome trafficking and bone resorption.

    Evidence Mutagenesis guided by the RUBICON RH-RAB7 crystal structure, co-IP, lysosome trafficking and bone resorption assays in osteoclasts

    PMID:38586475

    Open questions at the time

    • Relies on a homologous structure, not a direct PLEKHM1-RAB7 structure
    • Single point mutations failed to disrupt binding, complicating interface assignment
12. 2025 Medium

    Demonstrated that PLEKHM1 dosage is pathologically relevant by showing overexpression in substantia nigra impairs late-stage autophagy with p62 accumulation and reduced autolysosome maturation.

    Evidence rAAV PLEKHM1 overexpression in autophagy reporter mice with LAMP1/LC3/p62 markers

    PMID:40940751

    Open questions at the time

    • Mechanism by which excess PLEKHM1 stalls fusion not defined
    • Single lab; relevance to human neurodegeneration not established

• How the membrane-binding, RAB7-binding, HOPS-binding, and LIR activities of PLEKHM1 are integrated into a stepwise, regulated fusion cycle, and the structure of the native PLEKHM1-RAB7 complex, remain unresolved.
• No experimental PLEKHM1 structure
• Temporal coordination of partner engagement during a single fusion event undefined