Alternative titles; symbols
HGNC Approved Gene Symbol: NAE1
Cytogenetic location: 16q22.1 Genomic coordinates (GRCh38) : 16:66,802,878-66,830,976 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 16q22.1 | Neurodevelopmental disorder with dysmorphic facies and ischiopubic hypoplasia | 620210 | Autosomal recessive | 3 |
NAE1 encodes a subunit of the NEDD8 (603171)-activating enzyme (NAE), which controls the activity of the cullin-RING subtype of ubiquitin ligases (summary by Soucy et al., 2009). Covalent attachment of NEDD8 to target proteins is known as 'neddylation' and is an important mechanism for eukaryotic protein regulation (summary by Muffels et al., 2023).
Beta-amyloid precursor protein (APP; 104760) is a cell surface protein that has structural features characteristic of cell surface receptors with signal-transducing properties. To identify proteins with the potential to bind and interact with APP, Chow et al. (1996) used a C-terminal fragment of APP to screen a human fetal brain cDNA expression library. They isolated cDNAs encoding an APP-binding protein, which they designated APPBP1. Chow et al. (1996) demonstrated that the deduced 534-amino acid, 59-kD APPBP1 protein interacts with the C-terminal region of APP in in vitro binding assays and with full-length APP from mammalian cells in immunoprecipitation assays. The APPBP1 protein is 39% identical to the protein encoded by the Arabidopsis auxin resistance gene AXR1; both proteins are relatives of ubiquitin-activating enzyme-1 (UBE1; 314370). Northern blot analysis of human tissues revealed that the single-copy APPBP1 gene is ubiquitously expressed as a 1.8-kb transcript. In situ hybridization histochemistry showed that Appbp1 mRNA is expressed throughout the rat brain.
Chow et al. (1996) localized the APPBP1 gene to 16q22 by fluorescence in situ hybridization.
Ubiquitin (191339) is covalently attached to target proteins by a multienzymatic system consisting of E1 (ubiquitin-activating), E2 (ubiquitin-conjugating), and E3 (ubiquitin-ligating) enzymes. Osaka et al. (1998) found that NEDD8 (603171), a ubiquitin-like protein, is conjugated to proteins in a manner analogous to ubiquitylation. They found that APPBP1 can bind to NEDD8 in rabbit reticulocyte lysates. However, since APPBP1 shows similarity to only the N-terminal domain of an E1 enzyme, the authors reasoned that it must interact with a protein showing similarity to the C-terminal region of E1s. By searching sequence databases, Osaka et al. (1998) identified cDNAs encoding UBA3 (603172), the human homolog of yeast Uba3. In vitro, UBA3 formed a complex with APPBP1 and a thioester linkage with NEDD8. Osaka et al. (1998) suggested that the APPBP1/UBA3 complex functions as an E1-like enzyme for the activation of NEDD8.
Ts41 mutant Chinese hamster cells show a temperature-sensitive defect in the cell cycle and undergo successive S phases without intervening G2, M, and G1 phases. The phenotype suggests that the mutated gene negatively regulates entry into S phase and positively regulates entry into mitosis. Chen et al. (2000) showed that human APPBP1 corrected the ts41 defect. Overexpression of human APPBP1 in rat primary cortical neurons caused apoptosis, and this effect required the UBA3-binding domain of APPBP1. Dominant-negative human UBA3 and UBC12 (UBE2M; 603173) mutants inhibited the ability of APPBP1 to cause apoptosis, implicating the NEDD8 conjugation pathway. In addition, a specific caspase-6 (CASP6; 601532) inhibitor blocked APPBP1-induced apoptosis.
Walden et al. (2003) reported the structure and mutational analysis of human APPBP1-UBA3, the heterodimeric E1 enzyme for NEDD8. Each E1 activity is specified by a domain: an adenylation domain resembling bacterial adenylating enzymes, an E1-specific domain organized around the catalytic cysteine, and a domain involved in E2 recognition resembling ubiquitin. The domains are arranged around 2 clefts that coordinate protein and nucleotide binding so that each of E1's reactions drives the next, in an assembly-line fashion.
NEDD8 is first activated by an E1 enzyme, NEDD8-activating enzyme (NAE, a heterodimer of NAE1 and UBA3 subunits), transferred to an E2 enzyme (UBE2M), and then conjugated to target substrates. The NAE controls the activity of the cullin-RING subtype of ubiquitin ligases, thereby regulating the turnover of a subset of proteins upstream of the proteasome. Substrates of cullin-RING ligases have important roles in cellular processes associated with cancer cell growth and survival pathways. Soucy et al. (2009) described MLN4924, a potent and selective inhibitor of NAE. MLN4924 disrupts cullin-RING ligase-mediated protein turnover leading to apoptotic death in human tumor cells by a novel mechanism of action, the deregulation of S-phase DNA synthesis. MLN4924 suppressed the growth of human tumor xenografts in mice at compound exposures that were well tolerated. Soucy et al. (2009) concluded that NAE inhibitors may hold promise for the treatment of cancer.
Bohnsack and Haas (2003) purified APPBP1-UBA3 from human erythrocytes and analyzed the kinetics of NEDD8 activation. In the presence of radiolabeled ATP and radiolabeled recombinant NEDD8, APPBP1-UBA3 rapidly formed a stable stoichiometric ternary complex composed of tightly bound NEDD8 adenylate and UBA3-NEDD8 thiol ester. Isotope exchange kinetics showed that the heterodimer followed a pseudo-ordered mechanism with ATP the leading and NEDD8 the trailing substrate. Ala72 of NEDD8 was critical in binding APPBP1-UBA3. Bohnsack and Haas (2003) concluded that the mechanism of NEDD8 activation by APPBP1-UBA3 shows a high degree of conservation with ubiquitin activation by UBA1.
Huang et al. (2007) reported the structural analysis of a trapped ubiquitin-like protein (UBL) activation complex for the human NEDD8 pathway containing NEDD8's heterodimeric E1 (APPBP1-UBA3), 2 NEDD8s (1 thioester-linked to E1, 1 noncovalently associated for adenylation), a catalytically inactive E2 (UBC12), and MgATP. The results suggested that a thioester switch toggles E1-E2 affinities. Two E2 binding sites depend on NEDD8 being thioester-linked to E1. One is unmasked by a striking E1 conformational change. The other comes directly from the thioester-bound NEDD8. After NEDD8 transfer to E2, reversion to an alternate E1 conformation would facilitate release of the covalent E2-NEDD8 thioester product. Thus, Huang et al. (2007) concluded that transferring the UBL's thioester linkage between successive conjugation enzymes can induce conformational changes and alter interaction networks to drive consecutive steps in UBL cascades.
In 3 unrelated patients (patients 1-3) with neurodevelopmental disorder with dysmorphic facies and ischiopubic hypoplasia (NEDFIH; 620210), Muffels et al. (2023) identified homozygous or compound heterozygous missense mutations in the NAE1 gene (603385.0001-603385.0003) affecting highly conserved residues. The mutations, which were found by exome sequencing, were demonstrated to segregate with the disorder in 1 of the families (individual 1). Western blot analysis of fibroblasts from 2 patients showed an almost 80% reduction in NAE1 levels compared to controls; the parents of patient 1 had about 50% NAE1 abundance. Patient cells showed a reduction in the ratio of neddylated to non-neddylated cullin (e.g., CUL1, 603134), suggesting that NAE1 deficiency adversely affects function. Transcriptome analysis of patient fibroblasts showed evidence of proteasomal dysfunction with compensatory upregulation of alternative cellular protein degradation pathways. There was also a significant downregulation of genes involved in cartilage development, ossification, and chondrocyte differentiation, including SOX9 (608160) and RUNX2 (600211), which the authors postulated may result in altered endochondral bone development as observed in the patients. Patient CD3+ T cells showed perturbed NFKB (see 164011) signaling in response to stimulation, which may explain the infection-induced lymphopenia observed in some of the patients. Patient fibroblasts showed increased cellular toxicity and cell death when exposed to proteosome or neddylation inhibitors. Collectively, these data suggested that patients with NAE1 deficiency cannot adequately upregulate neddylation during periods of stress, which could explain the episodic stress-induced neurodegeneration observed in the patients.
In a 12-year-old girl (individual 1), born of unrelated Dutch parents, with neurodevelopmental disorder with dysmorphic facies and ischiopubic hypoplasia (NEDFIH; 620210), Muffels et al. (2023) identified compound heterozygous missense mutations at conserved residues in the NAE1 gene: a c.254G-A transition (c.254G-A, NM_003905.4), resulting in an arg85-to-gln (R85Q) substitution, and a c.147G-C transversion, resulting in a leu49-to-phe substitution (L49F; 603385.0002). The mutations, which were found by whole-exome sequencing, were each inherited from an unaffected parent. The R85Q variant was found 4 times in gnomAD, whereas L49F was found once. Query through the GeneMatcher program identified another patient, individual 2, a 19-year-old male also of Dutch descent, who carried a homozygous R85Q mutation that was identified through exome sequencing. Western blot analysis of fibroblasts from these 2 patients showed an almost 80% reduction in NAE1 levels compared to controls; the parents of patient 1 had about 50% NAE1 abundance. Patient cells showed a reduction in the ratio of neddylated to non-neddylated cullin (e.g., CUL1, 603134), suggesting that NAE1 deficiency adversely affects function. Patient 1 had drug-resistant seizures and lymphopenia associated with regression. Patient 2 did not have seizures, but showed lymphopenia during infection.
For discussion of the c.147G-C transversion (c.147G-C, NM_003905.4) in the NAE1 gene, resulting in a leu49-to-phe substitution (L49F), that was found in compound heterozygous state in a patient with neurodevelopmental disorder with dysmorphic facies and ischiopubic hypoplasia (NEDFIH; 620210) by Muffels et al. (2023), see 603385.0001.
In a 4-year-old boy (individual 3), born of consanguineous parents, with neurodevelopmental disorder with dysmorphic facies and ischiopubic hypoplasia (NEDFIH; 620210), Muffels et al. (2023) identified a homozygous c.1289G-A transition (c.1289G-A, NM_003905.4) in the NAE1 gene, resulting in an arg430-to-gln (R430Q) substitution at a highly conserved residue. The mutation was found by exome sequencing. The patient had infantile spasms and neurologic regression.
Bohnsack, R. N., Haas, A. L. Conservation in the mechanism of Nedd8 activation by the human AppBp1-Uba3 heterodimer. J. Biol. Chem. 278: 26823-26830, 2003. [PubMed: 12740388] [Full Text: https://doi.org/10.1074/jbc.M303177200]
Chen, Y., McPhie, D. L., Hirschberg, J., Neve, R. L. The amyloid precursor protein-binding protein APP-BP1 drives the cell cycle through the S-M checkpoint and causes apoptosis in neurons. J. Biol. Chem. 275: 8929-8935, 2000. [PubMed: 10722740] [Full Text: https://doi.org/10.1074/jbc.275.12.8929]
Chow, N., Korenberg, J. R., Chen, X.-N., Neve, R. L. APP-BP1, a novel protein that binds to the carboxyl-terminal region of the amyloid precursor protein. J. Biol. Chem. 271: 11339-11346, 1996. [PubMed: 8626687] [Full Text: https://doi.org/10.1074/jbc.271.19.11339]
Huang, D. T., Hunt, H. W., Zhuang, M., Ohi, M. D., Holton, J. M., Schulman, B. A. Basis for a ubiquitin-like protein thioester switch toggling E1-E2 affinity. Nature 445: 394-398, 2007. [PubMed: 17220875] [Full Text: https://doi.org/10.1038/nature05490]
Muffels, I. J. J., Schene, I. F., Rehmann, H., Massink, M. P. G., van der Wal, M. M., Bauder, C., Labeur, M., Armando, N. G., Lequin, M. H., Houben, M. L., Giltay, J. C., Haitjema, S., and 13 others. Bi-allelic variants in NAE1 cause intellectual disability, ischiopubic hypoplasia, stress-mediated lymphopenia and neurodegeneration. Am. J. Hum. Genet. 110: 146-160, 2023. [PubMed: 36608681] [Full Text: https://doi.org/10.1016/j.ajhg.2022.12.003]
Osaka, F., Kawasaki, H., Aida, N., Saeki, M., Chiba, T., Kawashima, S., Tanaka, K., Kato, S. A new NEDD8-ligating system for cullin-4A. Genes Dev. 12: 2263-2268, 1998. [PubMed: 9694792] [Full Text: https://doi.org/10.1101/gad.12.15.2263]
Soucy, T. A., Smith, P. G., Milhollen, M. A., Berger, A. J., Gavin, J. M., Adhikari, S., Brownell, J. E., Burke, K. E., Cardin, D. P., Critchley, S., Cullis, C. A., Doucette, A., and 23 others. An inhibitor of NEDD8-activating enzyme as a new approach to treat cancer. Nature 458: 732-736, 2009. [PubMed: 19360080] [Full Text: https://doi.org/10.1038/nature07884]
Walden, H., Podgorski, M. S., Schulman, B. A. Insights into the ubiquitin transfer cascade from the structure of the activating enzyme for NEDD8. Nature 422: 330-334, 2003. [PubMed: 12646924] [Full Text: https://doi.org/10.1038/nature01456]