ATP6V1A

ATP6V1A encodes the catalytic A subunit of the V1 domain of the vacuolar H+-ATPase (V-ATPase), which hydrolyzes ATP to drive proton translocation across intracellular membranes and is essential for lysosomal acidification, autophagy flux, vesicular trafficking, and synaptic plasticity. The subunit is regulated post-translationally by AMPK phosphorylation at Ser-384, which inhibits proton secretion and causes cytoplasmic redistribution (PMID:23863464), and by mTORC1 phosphorylation at Ser-441, which promotes stabilization through interaction with αB-crystallin at lysosomes; loss of this stabilization leads to ubiquitin–proteasome-mediated degradation and elevated lysosomal pH (PMID:31786107), a pathway also engaged by CISH-mediated ubiquitination (PMID:41522347). De novo heterozygous missense mutations in ATP6V1A cause developmental epileptic encephalopathy through either gain-of-function (hyperacidification) or loss-of-function (impaired acidification) effects on lysosomes, while biallelic mutations cause autosomal-recessive cutis laxa linked to disrupted V-ATPase complex assembly and Golgi trafficking defects (PMID:29668857, PMID:28065471, PMID:35675510). In neurons, ATP6V1A depletion impairs lysosomal pH regulation, blocks autophagy progression, reduces neurite elongation and excitatory synaptic input, and prevents synaptic rearrangement upon plasticity induction (PMID:38837572, PMID:29668857).

1. 1988 High

   Establishing that the V-ATPase subunit A contains the catalytic ATP hydrolysis site resolved a key question about which subunit drives proton pumping, grounding all subsequent functional studies of ATP6V1A.

   Evidence Gene cloning and sequence homology analysis of Neurospora crassa vma-1 revealing a conserved nucleotide-binding region

   PMID:2971651

   Open questions at the time

   • No direct biochemical demonstration of ATP hydrolysis by purified subunit A alone
   • Mammalian ortholog not yet characterized
2. 1992 High

   Defining the protein splicing mechanism of the yeast VMA1 intein established that specific cysteine residues catalyze an autocatalytic excision reaction required to generate the functional 69-kDa subunit A — a unique post-translational processing event among ATPase subunits.

   Evidence Site-directed mutagenesis of Cys-284 and Cys-738 in yeast, in vitro reconstitution of splicing, and X-ray crystallography (2.1 Å) of the intein precursor revealing the N→S acyl shift mechanism

   PMID:11884132 PMID:1417861 PMID:8651930

   Open questions at the time

   • Intein splicing is specific to yeast/fungal VMA1 and does not occur in metazoan ATP6V1A
   • Regulation of splicing efficiency in vivo not fully understood
3. 2007 High

   Demonstrating that atp6v1a knockdown in zebrafish abolishes acid secretion and disrupts ion homeostasis in vivo established the subunit's non-redundant role in organismal physiology beyond yeast genetics.

   Evidence Morpholino antisense knockdown in zebrafish with in vivo acid secretion and ion measurements

   PMID:17272665

   Open questions at the time

   • Morpholino approach cannot distinguish cell-autonomous from systemic effects
   • Mammalian in vivo loss-of-function not yet performed at this stage
4. 2013 High

   Identifying AMPK as a direct kinase phosphorylating ATP6V1A at Ser-384 revealed the first post-translational regulatory switch controlling V-ATPase membrane targeting and proton secretion, linking cellular energy sensing to pump activity.

   Evidence In vitro kinase assay, mass spectrometry site identification, S384A mutagenesis, H+ secretion assay in perfused kidney collecting duct and HEK-293 cells

   PMID:23863464

   Open questions at the time

   • Whether Ser-384 phosphorylation regulates V-ATPase in non-renal tissues was untested
   • Structural basis for how phosphorylation disrupts membrane association unknown
5. 2017 High

   Linking biallelic ATP6V1A missense mutations to autosomal-recessive cutis laxa — with complexome profiling showing disrupted V-ATPase assembly and functional assays revealing impaired Golgi retrograde trafficking — established ATP6V1A as a disease gene and connected it to vesicular trafficking beyond lysosomes.

   Evidence Whole-exome sequencing, BN-PAGE/LC-MS/MS complexome profiling, brefeldin A transport assay, electron microscopy in patient fibroblasts

   PMID:28065471

   Open questions at the time

   • How specific missense mutations differentially affect V1–V0 assembly versus catalytic activity not resolved
   • No animal model recapitulating cutis laxa phenotype at this time
6. 2018 High

   Characterizing de novo heterozygous ATP6V1A mutations revealed that gain-of-function and loss-of-function variants cause opposing lysosomal pH changes yet both impair autophagosome recruitment and neuronal function, establishing the mechanistic basis of developmental epileptic encephalopathy and showing that precise V-ATPase activity is required for neuronal health.

   Evidence LysoTracker/LysoSensor fluorescence, cycloheximide chase, autophagosome recruitment assay, neurite morphology and synaptic input measurements in HEK293T cells, patient lymphoblasts, and primary rat neurons

   PMID:29668857

   Open questions at the time

   • How gain-of-function mutations mechanistically increase proton pumping not defined
   • Patient-specific neuronal models (iPSC) not yet fully developed at this stage
7. 2019 High

   Discovery that mTORC1 phosphorylates ATP6V1A at Ser-441 to promote αB-crystallin binding and protect it from proteasomal degradation established a second signaling axis (mTORC1–αB-crystallin) controlling V-ATPase stability at lysosomes, complementing the AMPK pathway.

   Evidence GST pull-down, co-immunoprecipitation, S441A mutagenesis, rapamycin treatment, lysosome fractionation, zebrafish HSF4 knockdown model

   PMID:31786107

   Open questions at the time

   • Whether mTORC1-mediated stabilization operates in neurons or immune cells not tested
   • E3 ligase mediating ATP6V1A ubiquitination in this context not identified
8. 2022 High

   Extending genotype–phenotype correlations across multiple ATP6V1A variants in patient fibroblasts and iPSC-derived neurons confirmed that phenotype severity scales with the direction and magnitude of lysosomal pH disruption, and revealed ultrastructural pathology (electron-dense inclusions, small lysosomes) in human neurons.

   Evidence LysoTracker staining, LAMP1 immunoblotting, organelle pH measurement, substrate accumulation assay, electron microscopy in patient fibroblasts and iPSC-derived neurons

   PMID:35675510

   Open questions at the time

   • Molecular basis for differential assembly defects of individual variants not structurally resolved
   • Whether lysosomal storage material composition differs between variants unknown
9. 2024 High

   Demonstrating that Atp6v1a depletion in primary hippocampal neurons blocks autophagy progression, causes aberrant lysosome accumulation, and prevents synaptic rearrangement upon plasticity induction directly linked V-ATPase catalytic subunit function to synaptic plasticity mechanisms.

   Evidence shRNA knockdown in murine hippocampal neurons, electrophysiology, electron microscopy, autophagy flux assays

   PMID:38837572

   Open questions at the time

   • Whether synaptic phenotypes are cell-autonomous or involve non-cell-autonomous signaling not determined
   • In vivo conditional knockout model in brain not yet reported
10. 2025 Medium

    Identifying CISH as an E3 ligase adaptor that ubiquitinates ATP6V1A for proteasomal degradation, downstream of AHR transcriptional activation, defined a third regulatory axis controlling V-ATPase protein levels and connected ATP6V1A turnover to immune microenvironment signaling.

    Evidence ChIP for AHR binding to CISH promoter, CISH siRNA, ubiquitination assay, lysosomal pH measurement, in vivo mouse pregnancy model

    PMID:41522347

    Open questions at the time

    • Whether CISH directly ubiquitinates ATP6V1A or acts through a complex is not distinguished
    • Relevance outside decidual macrophages not established
    • Single study without independent replication

• Key unresolved questions include the structural basis for how specific disease-causing missense mutations alter V-ATPase catalytic activity or assembly, whether the multiple regulatory phosphorylation and ubiquitination pathways converge on a common mechanism of V1–V0 dissociation, and whether in vivo conditional knockout in mammalian brain recapitulates the synaptic and epileptic phenotypes seen in patients.
• No high-resolution structure of mammalian V-ATPase with disease mutations
• No conditional brain-specific Atp6v1a knockout mouse model reported
• Crosstalk between AMPK, mTORC1, and CISH regulatory axes on the same subunit unexplored