ATP6V1A

ATP6V1A encodes the catalytic A subunit of the vacuolar-type H+-ATPase (V-ATPase) V1 domain, the ATP-hydrolyzing engine that drives proton pumping to acidify lysosomes, endosomes, and other intracellular compartments and to mediate extracellular acid secretion (PMID:2139027, PMID:17272665). In yeast, the founding ortholog VMA1 was shown to harbor the ATP hydrolysis active site and to mature through an autocatalytic protein-splicing reaction in which an internal ~454-residue intein is excised and the flanking exteins are ligated to yield the active subunit; this splicing depends on junction cysteines and conserved histidines and proceeds via an N→S acyl shift forming a thiazolidine intermediate (PMID:2139027, PMID:1417861, PMID:9188457, PMID:11884132, PMID:14646148). Proper incorporation of the A subunit into the V-ATPase holoenzyme is required for lysosomal pH homeostasis, vesicular trafficking, and autophagy flux: biallelic missense mutations impair complex assembly/stability and retrograde trafficking and cause autosomal-recessive cutis laxa (PMID:28065471), while de novo heterozygous mutations cause developmental encephalopathy with epilepsy through either loss-of-function (reduced expression via increased degradation, elevated lysosomal pH) or gain-of-function (excess organellar proton pumping), both impairing autophagosomal V-ATPase recruitment, neurite elongation, and excitatory synaptic input (PMID:29668857, PMID:35675510). Consistent with this, neuronal Atp6v1a depletion disrupts lysosomal acidification and autophagy, producing aberrant somatic lysosomes and synaptic defects in plasticity (PMID:38837572). ATP6V1A activity and abundance are tuned by multiple inputs: AMPK directly phosphorylates Ser-384 to inhibit proton secretion and redistribute the V-ATPase in response to metabolic state (PMID:23863464), whereas mTORC1 phosphorylates Ser-441 to promote αB-crystallin binding that stabilizes the subunit against proteasomal degradation (PMID:31786107). Protein abundance is further controlled at the transcriptional level by YY1 (activating) and HIF-1α (repressing under hypoxia) and post-translationally by CISH-driven ubiquitination (PMID:28592880, PMID:36748335, PMID:41522347). ATP6V1A also supports microglial phagocytic degradation through interaction with GPNMB and is exploited by rabies virus, whose matrix protein binds the subunit's middle domain to facilitate virion uncoating (PMID:39992792, PMID:33208464).

1. 1990 High

   Establishing that the V-ATPase A subunit gene encodes the catalytic ATP-hydrolysis subunit and undergoes an unprecedented internal-domain excision defined the protein's core enzymatic identity and its unusual maturation.

   Evidence Cloning, sequencing, and peptide mapping of yeast VMA1

   PMID:2139027

   Open questions at the time

   • Did not resolve the chemical mechanism of the splicing reaction
   • Catalytic residues for ATP hydrolysis not mapped in this study
2. 1997 High

   Identifying junction cysteines and conserved histidines as essential for splicing, and confirming splicing as a folding-dependent intramolecular autocatalytic reaction, defined the catalytic logic of intein excision.

   Evidence Site-directed and random mutagenesis with functional readout in null yeast and bacteria; in vitro refolding splicing assay; intragenic suppressor genetics

   PMID:1417861 PMID:8651930 PMID:9188457 PMID:9276458 PMID:9286669

   Open questions at the time

   • Atomic geometry of the reaction intermediate not yet resolved
   • Relevance of splicing to mammalian ATP6V1A not addressed
3. 2002 High

   The 2.1 Å crystal structure of the spliceable precursor captured the N→S acyl shift and transesterification chemistry, providing the atomic mechanism of protein splicing.

   Evidence X-ray crystallography of a mutant precursor bearing N- and C-extein residues

   PMID:11884132 PMID:14646148

   Open questions at the time

   • Structure is of the intein/extein precursor, not the assembled V-ATPase A subunit
   • No mammalian structural counterpart
4. 2007 High

   In vivo knockdown showing loss of acid secretion and ion imbalance established ATP6V1A as physiologically required for vertebrate epithelial proton transport and ion homeostasis.

   Evidence Morpholino knockdown in zebrafish embryos with pH-dye acid-secretion and ion-content assays

   PMID:17272665

   Open questions at the time

   • Morpholino off-target effects not excluded
   • Tissue-specific mechanism in mammals not addressed
5. 2013 High

   Demonstrating AMPK phosphorylation of Ser-384 as inhibitory linked V-ATPase activity directly to cellular metabolic status, defining the first post-translational regulatory input.

   Evidence Mass spectrometry site mapping, in vitro kinase assay, S384A mutant rescue, perfused collecting duct and HEK293 acidification assays, localization imaging

   PMID:23863464

   Open questions at the time

   • Structural basis for how Ser-384 phosphorylation alters pumping not resolved
   • Interplay with other regulatory phosphosites unknown at the time
6. 2017 High

   Linking biallelic mutations to V-ATPase assembly/stability defects and trafficking impairment connected ATP6V1A dysfunction to a recessive connective-tissue disease (cutis laxa).

   Evidence Exome sequencing, complexome profiling, Brefeldin A retrograde transport, dermal TEM across five families

   PMID:28065471

   Open questions at the time

   • Mechanism linking lysosomal/V-ATPase defect to elastic fiber abnormality incomplete
   • Did not address dominant disease alleles
7. 2018 High

   Resolving that de novo heterozygous variants act through either loss-of-function or gain-of-function established a dual-mechanism basis for ATP6V1A developmental encephalopathy and tied it to autophagy and neuronal connectivity.

   Evidence HEK293T overexpression, LysoTracker/LysoSensor, degradation assays, hippocampal neuron transfection, structural modeling

   PMID:29668857

   Open questions at the time

   • Overexpression-based readouts may not reflect endogenous stoichiometry
   • How gain-of-function variants increase pumping mechanistically not resolved
8. 2019 High

   Identifying an mTORC1–αB-crystallin–ATP6V1A trimeric complex with S441 phosphorylation stabilizing the subunit revealed a degradation-control axis governing lysosomal acidification.

   Evidence GST pull-down, co-IP, lysosome fractionation, mTORC1 inhibition, S441A mutant, zebrafish HSF4-deficiency model

   PMID:31786107

   Open questions at the time

   • Ubiquitin ligase mediating degradation not identified
   • Generalizability beyond lens epithelium untested
9. 2020 High

   Mapping a direct interaction between the ATP6V1A middle domain and rabies matrix protein showed the subunit is co-opted for viral uncoating, extending its role to host–pathogen biology.

   Evidence Interactome mapping, reciprocal co-IP, domain mapping, knockdown/overexpression and trans-complementation viral growth assays

   PMID:33208464

   Open questions at the time

   • Whether proton-pumping activity per se is required for uncoating not fully separated from binding
   • Relevance to other enveloped viruses untested
10. 2017 Medium

    Identifying YY1 as a direct transcriptional activator of the ATP6V1A promoter defined a transcriptional control point relevant to cancer cell V-ATPase expression.

    Evidence Promoter binding-site analysis, YY1 knockdown and overexpression with qRT-PCR/western in gastric cancer cells

    PMID:28592880

    Open questions at the time

    • Direct promoter occupancy by ChIP not shown
    • Physiological context of YY1 regulation beyond gastric cancer unknown
11. 2022 High

    Showing that severe versus mild patient variants produce opposite lysosomal pH phenotypes in patient-derived cells corroborated the loss-vs-gain dichotomy and revealed lysosomal ultrastructural pathology in patient neurons.

    Evidence LysoTracker/LysoSensor, LAMP1 immunoblot, TEM of patient fibroblasts and iPSC-derived neurons

    PMID:35675510

    Open questions at the time

    • Genotype-phenotype correlation mechanism for intermediate variants incomplete
    • In vivo neuronal consequences not directly measured
12. 2023 Medium

    Demonstrating HIF-1α-mediated repression of ATP6V1A under hypoxia linked the subunit to lysosome–multivesicular body fusion and rerouting of cargo into secreted extracellular vesicles.

    Evidence HIF-1α ChIP/reporter assays, knockdown/overexpression, lysosomal degradation and EV quantification in HNSCC cells

    PMID:36748335

    Open questions at the time

    • Single tumor-cell context
    • Whether EV redirection is direct consequence of V-ATPase loss or secondary not fully isolated
13. 2024 High

    Neuron-specific depletion tracing lysosomal acidification and autophagy defects to impaired neurite elongation and synaptic plasticity defined the cellular pathway from V-ATPase dysfunction to neuronal phenotype.

    Evidence shRNA knockdown in primary murine hippocampal neurons with electrophysiology, EM, live imaging, pH and autophagy assays

    PMID:38837572

    Open questions at the time

    • In vivo behavioral consequences not addressed
    • Distinction between autophagy block and direct synaptic pH role not fully separated
14. 2025 Medium

    Identifying a GPNMB–ATP6V1A interaction required for microglial phagocytosis, rescuable by ATP6V1A activation, extended the subunit's role to immune clearance of neuronal debris and amyloid.

    Evidence Co-IP, GPNMB knockout mice, pharmacological ATP6V1A activation, phagocytosis and lysosomal degradation assays

    PMID:39992792

    Open questions at the time

    • Single lab; reciprocal interaction not extensively validated
    • Molecular basis of GPNMB-ATP6V1A binding not mapped
15. 2026 Medium

    Showing that AHR-induced CISH drives ubiquitination and degradation of ATP6V1A, triggering mtDNA release via cGAS-STING, identified a ubiquitin-proteasome control axis with inflammatory consequences.

    Evidence Co-IP, ubiquitination assays, AHR ChIP at CISH promoter, knockdown, lysosomal pH and mtDNA assays, mouse pregnancy model

    PMID:41522347

    Open questions at the time

    • Direct E3 ligase activity of CISH on ATP6V1A vs adaptor role not fully distinguished
    • Generalizability beyond decidual macrophages untested

• How the multiple regulatory inputs (AMPK Ser-384, mTORC1 Ser-441, αB-crystallin, YY1, HIF-1α, CISH) are integrated in vivo to set V-ATPase activity in distinct tissues remains unresolved.
• No unified model of how phosphorylation, complex stabilization, and degradation pathways are coordinated
• Tissue-specific dominance of each regulatory axis unknown
• No high-resolution structure of mammalian ATP6V1A within the assembled holoenzyme