NAA60

NAA60 (NatF) is a Golgi-localized N-terminal acetyltransferase that co- and post-translationally acetylates Met-starting N-termini of transmembrane proteins whose cytosolic tails face the cytoplasm, thereby controlling their surface trafficking, Golgi structural integrity, and chromosome segregation (PMID:21750686, PMID:25732826). The enzyme is anchored to the cytosolic face of medial/trans-Golgi membranes as a peripheral membrane protein via two C-terminal amphipathic helices that fold upon contact with PI(4)P-enriched lipid bilayers, and its GNAT-domain catalytic mechanism depends on Tyr97 and His138 (PMID:28196861, PMID:27550639). Functionally validated substrates include the phosphate importer SLC20A2 and the volume-regulated anion channel subunits LRRC8A/LRRC8D, whose Nt-acetylation by NAA60 promotes surface expression and channel-mediated drug uptake, respectively (PMID:38480682, PMID:41053424). Biallelic loss-of-function variants in NAA60 cause autosomal recessive primary familial brain calcification through impaired SLC20A2 surface delivery and phosphate homeostasis (PMID:38480682).

1. 2011 High

   Identification of NAA60 as a novel NAT with Met-starting substrate specificity and a role in chromosome segregation established a previously unrecognized acetyltransferase activity distinct from known NatA–E complexes.

   Evidence In vitro peptide library acetylation, yeast ectopic expression with N-terminal COFRADIC, and Drosophila RNAi showing segregation defects

   PMID:21750686

   Open questions at the time

   • Endogenous substrates in metazoan cells were not identified
   • Mechanism linking Nt-acetylation to chromosome segregation was unresolved
   • Subcellular localization in mammalian cells was not yet characterized
2. 2011 Medium

   An independent study reported NAA60 (HAT4) as a Golgi-localized lysine acetyltransferase for histone H4 (K79, K91), linking it to nucleosome assembly and DNA damage sensitivity, though its KAT activity has not been widely replicated.

   Evidence In vitro HAT assay with free histone H4; siRNA depletion with proliferation, apoptosis, and DNA damage readouts

   PMID:21981917

   Open questions at the time

   • KAT activity toward histone H4 has not been independently confirmed by other groups
   • Whether Golgi-localized NAA60 encounters free histone H4 in a physiological context is unclear
   • Relationship between KAT and NAT activities remains unresolved
3. 2015 High

   Demonstrating that NAA60 resides on the cytosolic face of Golgi membranes and specifically acetylates transmembrane proteins with cytosol-facing N-termini resolved its substrate class and explained why its loss fragments the Golgi.

   Evidence PROMPT topology assay, selective permeabilization, Nt-acetylome proteomics after siRNA knockdown, and Golgi morphology imaging

   PMID:25732826

   Open questions at the time

   • The molecular mechanism by which loss of Nt-acetylation leads to Golgi fragmentation was not determined
   • How NAA60 is recruited to and retained at the Golgi membrane was unknown
4. 2016 High

   Crystal structures of NAA60 with Acetyl-CoA/CoA revealed the catalytic mechanism (Tyr97/His138) and an amphipathic helix contributing to Golgi targeting, providing an atomic-level framework for understanding substrate recognition and membrane association.

   Evidence X-ray crystallography with active-site mutagenesis and enzymatic assays

   PMID:27550639

   Open questions at the time

   • No co-crystal with a peptide substrate to define the substrate-binding groove
   • Full membrane-anchoring mechanism was not yet established from the structure alone
5. 2017 High

   Identification of two C-terminal amphipathic helices that fold on PI(4)P-containing membranes explained the selective Golgi residency of NAA60 and established it as a peripheral rather than integral membrane protein.

   Evidence Liposome-binding assays, PI(4)P-specificity lipid binding, and cellular mutagenesis of hydrophobic helix faces

   PMID:28196861

   Open questions at the time

   • Whether additional protein–protein interactions contribute to Golgi retention was not tested
   • Regulation of NAA60 membrane association under signaling or stress conditions was not examined
6. 2024 High

   Linking NAA60 to primary familial brain calcification through biallelic loss-of-function variants and showing that NAA60 directly Nt-acetylates SLC20A2 to promote its surface expression and phosphate uptake provided the first disease mechanism and a defined physiological substrate–function axis.

   Evidence In vitro Nt-acetylation of SLC20A2, surface biotinylation, phosphate uptake assays in NAA60 KO cells, and patient variant analysis

   PMID:38480682

   Open questions at the time

   • Whether Nt-acetylation affects SLC20A2 folding, stability, or trafficking specifically is unresolved
   • Animal model confirmation of the PFBC phenotype was not reported in this study
7. 2024 Medium

   An independent study on a patient frameshift variant confirmed that disease-causing NAA60 mutations mislocalise from the Golgi and undergo accelerated degradation, and proteomics of NAA60 KO cells revealed broader changes in brain calcification-associated membrane proteins.

   Evidence Immunofluorescence, co-immunoprecipitation, and mass spectrometry in NAA60 KO cell lines

   PMID:39229657

   Open questions at the time

   • Co-IP interactions with PiT2 and XPR1 lack reciprocal validation
   • Downstream proteomic changes could be indirect consequences of Golgi dysfunction
8. 2025 Medium

   BioID proximity labeling refined NAA60 to the medial/trans-Golgi and identified golgins and GRASP proteins as proximal partners, providing a molecular context for how NAA60 loss disrupts Golgi architecture.

   Evidence BioID with streptavidin purification, mass spectrometry, and sub-organellar imaging

   PMID:39965656

   Open questions at the time

   • Proximity partners have not been validated as direct physical interactors or substrates
   • Whether NAA60 acetylates golgins/GRASPs or merely co-resides with them is unknown
9. 2025 Medium

   Demonstrating that NAA60 Nt-acetylates LRRC8A/D to facilitate platinum drug uptake through VRAC channels extended its functional repertoire beyond phosphate homeostasis to chemoresistance and ion channel regulation.

   Evidence NAA60 KO cells, N-terminal mutagenesis of LRRC8A/D, platinum uptake/cytotoxicity assays, and in vivo tumor models

   PMID:41053424

   Open questions at the time

   • Structural basis for how Nt-acetylation alters VRAC channel permeability is unresolved
   • Whether this mechanism operates in non-BRCA1 contexts has not been tested

• How Nt-acetylation by NAA60 mechanistically governs the trafficking, stability, or activity of its transmembrane substrates — and the full catalogue of in vivo substrates — remains incompletely defined.
• No substrate-bound co-crystal structure exists to explain selectivity
• Whether NAA60 KAT activity toward histone H4 is physiologically relevant remains unresolved
• Animal models recapitulating PFBC or Golgi fragmentation phenotypes have not been reported