Alternative titles; symbols
HGNC Approved Gene Symbol: NSUN3
Cytogenetic location: 3q11.2 Genomic coordinates (GRCh38): 3:94,063,061-94,131,832 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 3q11.2 | Combined oxidative phosphorylation deficiency 48 | 619012 | Autosomal recessive | 3 |
NSUN3 is a S-adenosylmethionine-dependent 5-methylcytosine (m5C) methyltransferase (EC 2.1.1.203) that is required for modification of cytosine in the wobble position (C34) of mitochondrial tRNA(met) (MTTM; 590065). This modification of C34 is critical for subsequent oxidative conversion of m5C to 5-formylcytosine (f5C) and mitochondrial protein synthesis (Van Haute et al., 2016).
By immunohistochemical analysis, cell fractionation, and protease digestion, Van Haute et al. (2016) determined that NSUN3 localized within mitochondria in human cell lines.
Independently, Nakano et al. (2016) showed that NSUN3 is a mitochondrial protein. Western blot analysis detected human NSUN3 at an apparent molecular mass similar to its theoretical mass of 38 kD, suggesting that NSUN3 is not proteolytically processed after mitochondrial import.
Using proteinase K experiments, Haag et al. (2016) localized NSUN3 to mitochondrial matrix in human cells.
MTTM decodes AUG and the nontraditional AUA, AUU, and AUC codons. Decoding of these codons and subsequent mitochondrial protein synthesis requires f5C34 in the wobble position of MTTM. Van Haute et al. (2016) determined that NSUN3 is required for deposition of m5C at C34 within the anticodon loop in MTTM. Deficiency of m5C34 in MTTM resulted in lack of f5C34 and defective mitochondrial translation and oxidative phosphorylation. NSUN3 showed much lower m5C activity with other mitochondria-encoded RNAs compared with MTTM.
Independently, Nakano et al. (2016) showed that NSUN3 mediated formation of m5C34 in MTTM. In vitro, formation of m5C34 by recombinant human NSUN3 required addition of S-adenosylmethionine. Knockout (KO) of NSUN3 resulted in HEK293T cells that were unable to grow in galactose-containing medium. NSUN3-KO cells showed reduced oxygen consumption rate and reduced protein synthesis, with defective assembly of respiratory chain complex I. Nakano et al. (2016) concluded that NSUN3 is required for MTTM recognition of AUA codons as initiation methionines and for mitochondrial protein synthesis, oxidative phosphorylation, and respiratory function.
Haag et al. (2016) confirmed the C34 wobble nucleotide in MTTM as the endogenous target of human NSUN3 and that NSUN3 generates the m5C moiety at C34 in MTTM. They found that mitochondrial ALKBH1 (605345) oxidized m5C34 to f5C34 in the presence of alpha-ketoglutarate and Fe(2+).
Nakano et al. (2016) determined that NSUN3 has 6 exons, the first of which is noncoding.
Hartz (2017) mapped the NSUN3 gene to chromosome 3q11.2 based on an alignment of the NSUN3 sequence (GenBank AK026262) with the genomic sequence (GRCh38).
In a male infant, born of unrelated German parents, with combined oxidative phosphorylation deficiency-48 (COXPD48; 619012), Van Haute et al. (2016) identified compound heterozygous loss-of-function mutations in the NSUN3 gene (617491.0001 and 617491.0002). Western blot analysis of patient-derived fibroblasts showed absence of the full-length NSUN3 protein, consistent with a loss of function. Patient fibroblasts also showed impaired mitochondrial respiratory chain activity, reduced oxygen consumption, impaired growth under galactose conditions, and defective mitochondrial translation and protein synthesis compared to controls. These defects could be restored by expression of wildtype NSUN3. More detailed analysis of patient cells showed methylation abnormalities affecting the anticodon of mt-tRNA(Met), which was responsible for impaired mitochondrial translation and a combined OXPHOS deficiency.
In an 8-month-old boy, born of consanguineous East Asian parents, with COXPD48, Paramasivam et al. (2020) identified compound heterozygous missense mutations in the NSUN3 gene (C152S, 617491.0003 and A141P, 617491.0004). The mutations, which were found by targeted sequencing and confirmed by Sanger sequencing, segregated with the disorder in the family. Both occurred at highly conserved residues in the protein and neither were present in several public databases, including gnomAD. Functional studies of the variant and studies of patient cells were not performed.
In a male infant, born of unrelated German parents, with combined oxidative phosphorylation deficiency-48 (COXPD48; 619012), Van Haute et al. (2016) identified compound heterozygous loss-of-function mutations in the NSUN3 gene: a 3.1-kb deletion (c.123-615_466+2155del, NM_022072.3), removing exon 3 and generating aberrant splicing, resulting in a frameshift and premature termination (Glu42ValfsTer11), and a c.295C-T transition, resulting in an arg99-to-ter (R99X; 617491.0002) substitution. The mutations, which were found by whole-exome sequencing, segregated with the disorder in the family. Western blot analysis of patient-derived fibroblasts showed absence of the full-length NSUN3 protein, consistent with a loss of function. Patient fibroblasts also showed impaired mitochondrial respiratory chain activity, reduced oxygen consumption, impaired growth under galactose conditions, and defective mitochondrial translation and protein synthesis compared to controls. These defects could be restored by expression of wildtype NSUN3.
For discussion of the c.295C-T transition (c.295C-T, NM_022072.3) in the NSUN3 gene, resulting in an arg99-to-ter (R99X) substitution, that was found in compound heterozygous state in a patient with combined oxidative phosphorylation deficiency-48 (COXPD48; 619012) by Van Haute et al. (2016), see 617491.0001.
In an 8-month-old boy, born of consanguineous East Asian parents, with combined oxidative phosphorylation deficiency-48 (COXPD48; 619012), Paramasivam et al. (2020) identified compound heterozygous missense mutations in exon 3 of the NSUN3 gene: a c.454T-A transversion, resulting in a cys152-to-ser (C152S) substitution, and a c.421G-C transversion, resulting in an ala141-to-pro (A141P; 617491.0004) substitution. The mutations, which were found by targeted sequencing and confirmed by Sanger sequencing, segregated with the disorder in the family. Both occurred at highly conserved residues in the protein and neither were present in several public databases, including gnomAD. Functional studies of the variant and studies of patient cells were not performed.
For discussion of the c.421G-C transversion in the NSUN3 gene, resulting in an ala141-to-pro (A141P) substitution, that was found in compound heterozygous state in a patient with combined oxidative phosphorylation deficiency-48 (COXPD48; 619012) by Paramasivam et al. (2020), see 617491.0003.
Haag, S., Sloan, K. E., Ranjan, N., Warda, A. S., Kretschmer, J., Blessing, C., Hubner, B., Seikowski, J., Dennerlein, S., Rehling, P., Rodnina, M., Hobartner, C., Bohnsack, M. T. NSUN3 and ABH1 modify the wobble position of mt-tRNA(Met) to expand codon recognition in mitochondrial translation. EMBO J. 35: 2104-2119, 2016. [PubMed: 27497299] [Full Text: https://doi.org/10.15252/embj.201694885]
Hartz, P. A. Personal Communication. Baltimore, Md. 5/25/2017.
Nakano, S., Suzuki, T., Kawarada, L., Iwata, H., Asano, K., Suzuki, T. NSUN3 methylase initiates 5-formylcytidine biogenesis in human mitochondrial tRNA(Met). Nature Chem. Biol. 12: 546-551, 2016. [PubMed: 27214402] [Full Text: https://doi.org/10.1038/nchembio.2099]
Paramasivam, A., Meena, A. K., Venkatapathi, C., Pitceathly, R. D. S., Thangaraj, K. Novel biallelic NSUN3 variants cause early-onset mitochondrial encephalomyopathy and seizures. J. Molec. Neurosci. 70: 1962-1965, 2020. Erratum: J. Molec. Neurosci. 70: 1966 only, 2020. [PubMed: 32488845] [Full Text: https://doi.org/10.1007/s12031-020-01595-8]
Van Haute, L., Dietmann, S., Kremer, L., Hussain, S., Pearce, S. F., Powell, C. A., Rorbach, J., Lantaff, R., Blanco, S., Sauer, S., Kotzaeridou, U., Hoffmann, G. F., Memari, Y., Kolb-Kokocinski, A., Durbin, R., Mayr, J. A., Frye, M., Prokisch, H., Minczuk, M. Deficient methylation and formylation of mt-tRNA(Met) wobble cytosine in a patient carrying mutations in NSUN3. Nature Commun. 7: 12039, 2016. Note: Electronic Article. [PubMed: 27356879] [Full Text: https://doi.org/10.1038/ncomms12039]