Alternative titles; symbols
HGNC Approved Gene Symbol: LIG3
Cytogenetic location: 17q12 Genomic coordinates (GRCh38): 17:34,980,512-35,010,872 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 17q12 | Mitochondrial DNA depletion syndrome 20 (MNGIE type) | 619780 | Autosomal recessive | 3 |
Chen et al. (1995) purified DNA ligase II and DNA ligase III to near homogeneity from bovine liver and testis, respectively. Amino acid sequencing studies indicated that these enzymes are encoded by the same gene. Chen et al. (1995) isolated human and murine cDNA clones encoding DNA ligase III (LIG3) with probes based on the peptide sequences. The LIG3 cDNA encodes a polypeptide of 862 amino acids, whose sequence is more closely related to those of the DNA ligases encoded by poxviruses than to replicative DNA ligases, such as human DNA ligase I (126391).
Chen et al. (1995) mapped the LIG3 gene to human chromosome 17 by PCR analysis of a human-rodent somatic cell hybrid mapping panel. Wei et al. (1995) used fluorescence in situ hybridization to map the human DNA ligase III gene to human chromosome 17q11.2-q12.
Stumpf (2022) mapped the LIG3 gene to chromosome 17q12 based on an alignment of the LIG3 sequence (GenBank BC009026) with the genomic sequence (GRCh38).
Chen et al. (1995) observed elevated levels of DNA ligase III mRNA in primary spermatocytes undergoing recombination prior to the first meiotic division. Therefore, they suggested that DNA ligase III seals DNA strand breaks that arise during the process of meiotic recombination in germ cells and as a consequence of DNA damage in somatic cells.
Gao et al. (2011) reported that DNA ligase III is essential for mitochondrial DNA integrity but dispensable for nuclear DNA repair. Inactivation of ligase III in the mouse nervous system resulted in mtDNA loss leading to profound mitochondrial dysfunction, disruption of cellular homeostasis, and incapacitating ataxia. Similarly, inactivation of ligase III in cardiac muscle resulted in mitochondrial dysfunction and defective heart-pump function leading to heart failure. However, ligase III inactivation did not result in nuclear DNA repair deficiency, indicating that essential DNA repair repair functions of Xrcc1 (194360) can occur in the absence of ligase III. Instead, Gao et al. (2011) found that ligase I was critical for DNA repair, but acted in a cooperative manner with ligase III. Additionally, ligase III deficiency did not recapitulate the hallmark features of neural Xrcc1 inactivation such as DNA damage-induced cerebellar interneuron loss, further underscoring functional separation of these DNA repair factors. Therefore, Gao et al. (2011) concluded that the biological role of ligase III is to maintain mtDNA integrity and not Xrcc1-dependent DNA repair.
Simsek et al. (2011) demonstrated a crucial role for DNA ligase III in mitochondria but not in XRCC1-dependent repair. Simsek et al. (2011) used preemptive complementation to determine the viability requirement for Lig3 in mammalian cells and its requirement in DNA repair. Various forms of Lig3 were introduced stably into mouse embryonic stem cells containing a conditional allele of Lig3 that could be deleted with Cre recombinase. With this approach, Gao et al. (2011) found that the mitochondrial, but not nuclear, Lig3 is required for cellular viability. Although the catalytic function of Lig3 is required, the zinc finger and BRAC1 C-terminal-related domains of Lig3 are not. Remarkably, the viability requirement for Lig3 can be circumvented by targeting Lig1 to the mitochondria or expressing Chlorella virus DNA ligase, the minimal eukaryal nick-sealing enzyme, or Escherichia coli LigA, an NAD(+)-dependent ligase. Lig3-null cells are not sensitive to several DNA-damaging agents that sensitize Xrcc1-deficient cells. Simsek et al. (2011) concluded that their results established a role for Lig3 in mitochondria, but distinguished it from its interacting protein XRCC1.
In 7 patients from 3 unrelated families with mitochondrial DNA depletion syndrome-20 (MTDPS20; 619780), manifest as mitochondrial neurogastrointestinal encephalopathy syndrome (MNGIE), Bonora et al. (2021) identified compound heterozygous mutations in the LIG3 gene (600940.0001-600940.0006). The mutations, which were found by whole-exome sequencing, segregated with the disorder in the families. There were 3 missense, 2 nonsense, and 1 splice site mutation. None of the patients carried 2 truncating mutations. The mutations mapped to conserved domains in the gene; several affected functional regions. In vitro studies of patient fibroblasts, skeletal muscle, and cells transfected with some of the mutations showed that the mutations caused decreased LIG3 protein expression, disrupted mitochondrial morphology and function, impaired mtDNA ligase activity and mtDNA proliferation, and resulted in mtDNA depletion.
In 2 sibs, born of unrelated Italian parents, with MTDPS20, Invernizzi et al. (2021) identified compound heterozygous mutations in the LIG3 gene (600940.0007 and 600940.0008). The mutations, which were found by whole-exome and whole-genome sequencing, segregated with the disorder in the family. LIG3 transcripts were reduced and protein levels were about 56% of controls. Patient fibroblasts showed impaired recovery of induced mtDNA depletion.
Bonora et al. (2021) found that disruption or silencing of the zebrafish lig3 ortholog resulted in multiple abnormalities, including decreased cerebellar area, abnormal gut peristalsis, decreased intestinal goblet cells, reduced swim bladder area, decreased expression of mitochondrial markers, and eye abnormalities compared to controls.
The article by Moser et al. (2007) regarding the function of LIG3 and XRCC1 in nucleotide excision repair was retracted because an investigation at the Leiden University Medical Center concluded that 'unacceptable data manipulation by the last author Maria Fousteri led to breaches of scientific integrity, making these results unreliable.'
In 3 brothers (family 1) with mitochondrial DNA depletion syndrome-20 (MTDPS20; 619780), manifest as mitochondrial neurogastrointestinal encephalopathy syndrome (MNGIE), Bonora et al. (2021) identified compound heterozygous missense mutations in the LIG3 gene: a c.1611G-C transversion (c.1611G-C, NM_013975) in exon 9, predicted to result in a lys537-to-asn (K537N) substitution in the AdB domain, and a c.2890G-C transversion in exon 20, resulting in a gly964-to-arg (G964R; 600940.0002) substitution in the BRCT domain. The mutations, which were found by whole-exome sequencing, were not present in the gnomAD database. Each unaffected parent was heterozygous for 1 of the mutations, consistent with autosomal recessive inheritance. Analysis of patient fibroblasts demonstrated that the c.1611G-C transversion also altered splicing and caused the skipping of exon 9, resulting in a an in-frame deletion (495_537del) in the conserved ATP- and POLG (174763)-binding domains. Further in vitro studies indicated that this mutant protein was degraded and that the K537N protein was expressed at low levels; this variant protein showed a low affinity for POLG compared to controls. The G964R protein was also expressed at lower levels, suggesting protein instability, and had impaired nuclear localization in transfected cells. Patient skeletal muscle samples and fibroblasts showed significant mtDNA depletion compared to controls. This was associated with qualitative and quantitative mitochondrial defects, including fragmentation and decreased oxygen consumption and ATP production. However, mtDNA deletions were not observed. Neither K537N nor G964R was able to rescue the abnormal cerebellar phenotype observed in lig3-null zebrafish, further supporting the pathogenicity of these variants. The patients presented in childhood with profound gut dysmotility, recurrent pseudoobstructive episodes, skeletal muscle wasting, and leukoencephalopathy.
For discussion of the c.2890G-C transversion (c.2890G-C, NM_013975) in exon 20 of the LIG3 gene, resulting in a gly964-to-arg (G964R) substitution, that was found in compound heterozygous state in 3 sibs with mitochondrial DNA depletion syndrome-20 (MTDPS20; 619780), manifest as mitochondrial neurogastrointestinal encephalopathy syndrome (MNGIE), by Bonora et al. (2021), see 600940.0001.
In 2 Dutch sisters (family 2) with mitochondrial DNA depletion syndrome-20 (MTDPS20; 619780), manifest as mitochondrial neurogastrointestinal encephalopathy syndrome (MNGIE), Bonora et al. (2021) identified compound heterozygous mutations in the LIG3 gene: a c.799C-T transition (c.799C-T, NM_013975) in exon 4, resulting in an arg267-to-ter (R267X) substitution in the N-terminal DNA ligase domain, and a c.2996G-A transition in exon 20, resulting in a cys999-to-tyr (C999Y; 600940.0004) substitution in the BRCT domain. The mutations, which were found by whole-exome sequencing, segregated with the disorder in the family. Each unaffected parent was heterozygous for 1 of the mutations, consistent with autosomal recessive inheritance. R267X was present at a low frequency (2.0 x 10(-5)) in the gnomAD database, whereas C999Y was not present in gnomAD. Studies of patient fibroblasts showed that the R267X mutant was not expressed, consistent with nonsense-mediated mRNA decay. Western blot analysis showed a marked decrease in LIG3 levels, suggesting that the C999Y variant is unstable. Patient fibroblasts showed a severe defect in mtDNA repair with decreased ligase activity compared to controls. Patient skeletal muscle samples showed decreased mtDNA content at 66% compared to controls. The patients had onset of migraines, neurologic symptoms, and gastrointestinal dysmotility in the teenage years. They also had seizures and stroke-like episodes; 1 had leukoencephalopathy.
For discussion of the c.2996G-A transition (c.2996G-A, NM_013975) in exon 20 of the LIG3 gene, resulting in a cys999-to-tyr (C999Y; 600940.0004) substitution, that was found in compound heterozygous state in 2 sisters with mitochondrial DNA depletion syndrome-20 (MTDPS20; 619780), manifest as mitochondrial neurogastrointestinal encephalopathy syndrome (MNGIE), by Bonora et al. (2021), see 600940.0003.
In 2 brothers (family 3) with mitochondrial DNA depletion syndrome-20 (MTDPS20; 619780), manifest as mitochondrial neurogastrointestinal encephalopathy syndrome (MNGIE), Bonora et al. (2021) identified compound heterozygous mutations in the LIG3 gene: a c.1826C-T transition (c.1826C-T, NM_013975) in exon 12, resulting in a pro609-to-leu (P609L) substitution in the OB fold domain, and a c.2431C-T transition in exon 17, resulting in an arg811-to-ter (R811X; 600940.0006) substitution in the C-terminal DNA ligase domain. The mutations, which were found by whole-exome sequencing, segregated with the disorder in the family. Each unaffected grandparent was heterozygous for one of the mutations, consistent with autosomal recessive inheritance. Both variants were found at low frequencies in the gnomAD database (4.0 x 10(-6)). Analysis of patient fibroblasts showed that the R811X variant was not expressed. The P609L variant was predicted to destabilize the protein; lower LIG3 protein levels were found in patient cells and cells transfected with the P609L mutation compared to controls. Patient fibroblasts showed decreased capacity for mtDNA replication, in additional to defects in mtDNA repair. Mitochondrial DNA copy number was decreased in patient myoblasts, but normal in fibroblasts. These findings were associated with decreased oxygen consumption and increased mitochondrial reactive oxygen species in urothelial sediment cells (USC) compared to controls, confirming mitochondrial dysfunction. The brothers presented with refractory seizures in the first months of life. They had hypotonia, abnormal jerky movements, abdominal distension, and hepatomegaly, and were fed by NG tube. They met almost no developmental milestones; 1 died at 2 years of age. Brain imaging showed leukoencephalopathy and cerebellar atrophy.
For discussion of the c.2431C-T transition in exon 17 of the LIG3 gene, resulting in an arg811-to-ter (R811X) substitution, that was found in compound heterozygous state in 2 brothers with mitochondrial DNA depletion syndrome-20 (MTDPS20; 619780), manifest as mitochondrial neurogastrointestinal encephalopathy syndrome (MNGIE), by Bonora et al. (2021), see 600940.0005.
In 2 sibs, born of unrelated Italian parents, with mitochondrial DNA depletion syndrome-20 (MTDPS20; 619780), manifest as mitochondrial neurogastrointestinal encephalopathy syndrome (MNGIE), Invernizzi et al. (2021) identified compound heterozygous mutations in the LIG3 gene: a c.86G-A transition (c.86G-A, NM_013975.4), resulting in a trp29-to-ter (W29X) substitution in the mitochondrial targeting sequence, and a deep intronic G-to-A transition (c.1611+209G-A), resulting in aberrant splicing of exon 9 and premature termination (Ala539Ter). The mutations, which were found by whole-exome and whole-genome sequencing, segregated with the disorder in the family. LIG3 transcripts were reduced and protein levels were about 56% of controls. Patient fibroblasts showed impaired recovery of induced mtDNA depletion. The authors noted that the LIG3 gene contains 2 putative start codons, with the upstream ATG used for the mitochondrial isoform. Thus, the nuclear isoform may still be translated from the allele with the W29X mutation; the splice site mutation disrupts both isoforms. The patients had neonatal fatal myopathy and evidence of mitochondrial dysfunction.
For discussion of the G-to-A transition (c.1611+209G-A, NM_013975.4) in the LIG3 gene, resulting in aberrant splicing of exon 9 and premature termination (Ala539Ter), that was found in compound heterozygous state in 2 brothers with mitochondrial DNA depletion syndrome-20 (MTDPS20; 619780), manifest as mitochondrial neurogastrointestinal encephalopathy syndrome (MNGIE), by Invernizzi et al. (2021), see 600940.0007.
Bonora, E., Chakrabarty, S., Kellaris, G., Tsutsumi, M., Bianco, F., Bergamini, C., Ullah, F., Isidori, F., Liparulo, I., Diquigiovanni, C., Masin, L., Rizzardi, N., and 55 others. Biallelic variants in LIG3 cause a novel mitochondrial neurogastrointestinal encephalomyopathy. Brain 144: 1451-146, 2021. [PubMed: 33855352] [Full Text: https://doi.org/10.1093/brain/awab056]
Chen, J., Tomkinson, A. E., Ramos, W., Mackey, Z. B., Danehower, S., Walter, C. A., Schultz, R. A., Besterman, J. M., Husain, I. Mammalian DNA ligase III: molecular cloning, chromosomal localization, and expression in spermatocytes undergoing meiotic recombination. Molec. Cell. Biol. 15: 5412-5422, 1995. [PubMed: 7565692] [Full Text: https://doi.org/10.1128/MCB.15.10.5412]
Gao, Y., Katyal, S., Lee, Y., Zhao, J., Rehg, J. E., Russell, H. R., McKinnon, P. J. DNA ligase III is critical for mtDNA integrity but not Xrcc1-mediated nuclear DNA repair. Nature 471: 240-244, 2011. [PubMed: 21390131] [Full Text: https://doi.org/10.1038/nature09773]
Invernizzi, F., Legati, A., Nasca, A., Lamantea, E., Garavaglia, B., Gusic, M., Kopajtich, R., Prokisch, H., Zeviani, M., Lamperti, C., Ghezzi, D. Myopathic mitochondrial DNA depletion syndrome associated with biallelic variants in LIG3. Brain 144: e74, 2021. Note: Erratum: Brain 144: e88, 2021. [PubMed: 34165507] [Full Text: https://doi.org/10.1093/brain/awab238]
Moser, J., Kool, H., Giakzidis, I., Caldecott, K., Mullenders, L. H. F., Fousteri, M. I. Sealing of chromosomal DNA nicks during nucleotide excision repair requires XRCC1 and DNA ligase III-alpha in a cell-cycle-specific manner. Molec. Cell 27: 311-323, 2007. Note: Retraction: Molec. Cell 81: 5113 only, 2021. [PubMed: 17643379] [Full Text: https://doi.org/10.1016/j.molcel.2007.06.014]
Simsek, D., Furda, A., Gao, Y., Artus, J., Brunet, E., Hadjantonakis, A.-K., Van Houten, B., Shuman, S., McKinnon, P. J., Jasin, M. Crucial role for DNA ligase III in mitochondria but not in Xrcc1-dependent repair. Nature 471: 245-248, 2011. [PubMed: 21390132] [Full Text: https://doi.org/10.1038/nature09794]
Stumpf, A. M. Personal Communication. Baltimore, Md. 03/14/2022.
Wei, Y.-F., Robins, P., Carter, K., Caldecott, K., Pappin, D. J. C., Yu, G.-L., Wang, R.-P., Shell, B. K., Nash, R. A., Schar, P., Barnes, D. E., Haseltine, W. A., Lindahl, T. Molecular cloning and expression of human cDNAs encoding a novel DNA ligase IV and DNA ligase III, an enzyme active in DNA repair and recombination. Molec. Cell. Biol. 15: 3206-3216, 1995. [PubMed: 7760816] [Full Text: https://doi.org/10.1128/MCB.15.6.3206]