NAA40

NAA40 (NatD) is an N-terminal acetyltransferase that co-translationally acetylates the N-terminus of histones H4, H2A, and H2A.X, thereby establishing an epigenetic mark that controls downstream histone modifications, gene expression, and cellular metabolism. Cryo-EM structures show that NAA40 operates at the ribosomal peptide tunnel exit in a multienzyme complex with the NAC complex and METAP1, coordinating methionine removal with N-terminal acetylation (PMID:41820326). Within the nucleus, NAA40-mediated N-terminal acetylation antagonizes repressive marks such as H2A/H4S1ph and modulates H4R3me2s via transcriptional regulation of PRMT5, controlling expression of metabolic genes (TYMS), one-carbon metabolism, cellular acetyl-CoA levels, and de novo lipogenesis (PMID:30858358, PMID:34785778, PMID:35057804). NAA40 protein stability is regulated by RNF112-mediated ubiquitination and proteasomal degradation, and loss of NAA40 triggers p53-independent, caspase-9-mediated apoptosis in cancer cells (PMID:39757327, PMID:26666750).

1. 2016 High

   Establishing that NAA40 is required for cancer cell survival answered whether this acetyltransferase has pro-survival functions beyond histone modification: NAA40 depletion triggers mitochondrial apoptosis through caspase-9 independently of p53.

   Evidence siRNA knockdown in HCT116 and HT-29 CRC cells with caspase-9 inhibitor rescue and p53-null genetic control

   PMID:26666750

   Open questions at the time

   • Upstream signal linking loss of histone N-terminal acetylation to mitochondrial apoptosis initiation is unknown
   • Whether this apoptotic phenotype occurs in non-cancer cells was not tested
2. 2019 High

   Connecting NAA40-mediated N-terminal acetylation of H4 to downstream arginine methylation resolved how this modification communicates with the broader histone code: NAA40 depletion reduces H4R3me2s by transcriptionally downregulating PRMT5, linking N-acH4 to oncogene/tumor suppressor expression.

   Evidence NAA40 knockdown in CRC cell lines with histone mark measurement, PRMT5 expression analysis, and xenograft tumor growth assays

   PMID:30858358

   Open questions at the time

   • Whether NAA40 directly regulates PRMT5 transcription or acts through intermediate factors is unresolved
   • The full repertoire of genes regulated by the NAA40–PRMT5–H4R3me2s axis was not defined
3. 2021 High

   Demonstrating that NAA40 acetyltransferase activity controls one-carbon metabolism and chemoresistance revealed the metabolic consequences of histone N-terminal acetylation: NAA40 activates TYMS transcription by preventing repressive H2A/H4S1ph enrichment, connecting chromatin modification to 5-FU resistance.

   Evidence Transcriptomic and metabolomic profiling of NAA40-depleted CRC cells; acetyltransferase-dead mutant; ChIP for H2A/H4S1ph at TYMS promoter; xenograft 5-FU resistance assays

   PMID:34785778

   Open questions at the time

   • The kinase depositing H2A/H4S1ph in the absence of NAA40 was not identified
   • Whether the metabolic rewiring is reversible upon NAA40 re-expression was not fully tested
4. 2022 High

   Showing that NAA40 depletion elevates acetyl-CoA and promotes de novo lipogenesis broadened the metabolic scope of this enzyme from one-carbon metabolism to lipid homeostasis, conserved across mammalian hepatocytes and Drosophila fat body.

   Evidence Metabolomic and lipidomic profiling of NAA40-depleted murine hepatocytes; lipid droplet imaging; in vivo Drosophila fat body assay

   PMID:35057804

   Open questions at the time

   • The mechanism by which reduced histone N-terminal acetylation increases cytoplasmic acetyl-CoA pools remains unclear
   • Whether NAA40 directly acetylates non-histone substrates that affect metabolism was not addressed
5. 2025 Medium

   Identification of RNF112-mediated ubiquitination as a post-translational control mechanism for NAA40 protein levels established how NAA40 abundance is regulated, placing it downstream of an E3 ligase pathway in CRC.

   Evidence Co-IP/ubiquitination assays with RNF112 and NAA40 overexpression/knockdown rescue in CRC cells and xenografts

   PMID:39757327

   Open questions at the time

   • Specific ubiquitination sites on NAA40 were not mapped
   • Whether additional E3 ligases target NAA40 is unknown
   • Single-lab study awaits independent confirmation
6. 2025 Medium

   Demonstrating that NAA40 loss alters H3K4me3/H3K27me3 at the AGR2 promoter and that AGR2 partially rescues proliferation defects extended NAA40's transcriptional targets to include AGR2 and revealed crosstalk between N-terminal acetylation and canonical histone methylation marks in osteosarcoma.

   Evidence ChIP-qPCR, dual luciferase reporter, NAA40 knockdown with AGR2 rescue in osteosarcoma cells and in vivo animal experiments

   PMID:40020320

   Open questions at the time

   • How N-terminal acetylation loss leads to altered H3K4me3/H3K27me3 is mechanistically undefined
   • Single-lab study in one cancer type
   • Partial rescue by AGR2 implies additional NAA40 targets remain unidentified
7. 2025 High

   Identification of histone variant H2A.X as a bona fide NAA40 substrate expanded the enzyme's substrate repertoire and connected N-terminal acetylation to the DNA damage response, as the modification is dynamically regulated by UVB irradiation.

   Evidence In vitro acetyltransferase reconstitution, Co-IP, mass spectrometry detection of Nt-acH2A.X, UVB irradiation cell survival assay

   PMID:40665417

   Open questions at the time

   • Whether N-terminal acetylation of H2A.X affects canonical γH2A.X signaling is untested
   • The dynamics of Nt-acH2A.X during other forms of DNA damage are unknown
8. 2025 Medium

   AP-MS identification of nuclear interaction partners supported a dual-localization model for NAA40 — functioning both co-translationally at ribosomes and independently within the nucleus.

   Evidence Affinity purification coupled to mass spectrometry of nuclear NAA40

   PMID:40992843

   Open questions at the time

   • Nuclear interaction partners were not functionally validated
   • Whether nuclear NAA40 has distinct substrates from ribosomal NAA40 is unresolved
   • Single interactome study without reciprocal validation
9. 2026 High

   A cryo-EM structure of NAA40 at the ribosomal tunnel exit resolved the long-standing question of how co-translational histone N-terminal acetylation is organized: NAA40 binds the ribosome via the NAC complex and forms a tripartite complex with METAP1 that coordinates methionine excision with acetylation.

   Evidence Cryo-EM structural determination; biochemical reconstitution; ribosome-binding assays; mutagenesis of NAA40–NAC interface; in vitro acetyltransferase assay

   PMID:41820326

   Open questions at the time

   • Whether the NAA40–NAC–METAP1 complex processes all histone molecules or a subset is unknown
   • The kinetic parameters of the coupled methionine removal and acetylation reaction in cells remain unmeasured

• The mechanistic link between reduced histone N-terminal acetylation and elevated cytoplasmic acetyl-CoA — whether through altered acetyl-CoA consumption, metabolic gene expression, or both — remains unresolved, as does the identity of the full set of NAA40 nuclear substrates and partners.
• No structural model of nuclear NAA40 complexes exists
• Whether NAA40 acetylates non-histone substrates is untested
• The relative contribution of co-translational vs. nuclear NAA40 activity to cellular phenotypes is undefined