Alternative titles; symbols
HGNC Approved Gene Symbol: LIG1
Cytogenetic location: 19q13.33 Genomic coordinates (GRCh38): 19:48,115,445-48,170,344 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 19q13.33 | Immunodeficiency 96 | 619774 | Autosomal recessive | 3 |
LIG1 functions at the replication fork to join Okazaki fragments during replication of lagging strand DNA. LIG1 has also been implicated in nucleotide excision repair and in the long-patch form of base excision repair (summary by Harrison et al., 2002).
The major DNA ligase activity in proliferating mammalian cells is due to the high molecular mass enzyme DNA ligase I. From a Jurkat T-lymphoblast cDNA library, Barnes et al. (1990) cloned DNA ligase I, both by functional complementation of a Saccharomyces cerevisiae cdc9 mutation and by hybridization with oligonucleotide probes corresponding to peptide sequences of the purified bovine enzyme. Hybridization between the cloned sequences and mRNA and genomic DNA indicated that the human enzyme is transcribed from a single-copy gene. The deduced 919-amino acid protein has a predicted molecular mass of 102 kD. Northern blot analysis detected a 3.2-kb transcript. SDS-PAGE detected DNA ligase I at an apparent molecular mass of 125 kD.
Suzuki et al. (2002) reported that LIG1 is a transmembrane glycoprotein with an extracellular region composed of leucine-rich repeats and immunoglobulin-like domains. They stated that LIG1 is expressed predominantly in neural tissue. In situ hybridization detected mouse Lig1 expression in skin, predominantly in the upper part of hair follicles, with weaker expression in basal cells of epidermis.
Noguiez et al. (1992) demonstrated that the LIG1 gene has 28 exons spanning 53 kb of genomic DNA. The first exon is untranslated and uses a GC dinucleotide instead of the canonical GT splice donor. The 5-prime flanking region lacks a TATA box and is highly GC-rich, as is characteristic of 'housekeeping' genes. In common with the promoters of genes encoding other DNA replication enzymes, such as DNA polymerase alpha (312040), the 5-prime flanking region of the LIG1 gene contains recognition elements for several transcription factors that may mediate increased expression in quiescent cells in response to growth factors.
Lindahl and Barnes (1992) gave an extensive review of the mammalian DNA ligases.
Barnes et al. (1990) mapped the DNA ligase I gene to chromosome 19 by hybridization to DNAs from well-characterized rodent-human somatic cell hybrids retaining subsets of human chromosomes. By analysis of rodent-human somatic cell hybrids and by 2-color fluorescence in situ hybridization (FISH), Barnes et al. (1992) assigned the LIG1 gene to 19q13.2-q13.3 and demonstrated that it is distal to ERCC1 (126380). By FISH, Trask et al. (1993) assigned the LIG1 gene to 19q13.2-q13.3.
Using a mapping panel from an interspecific cross, Gariboldi et al. (1995) mapped the Lig1 gene to the centromeric part of mouse chromosome 7, a region homologous to human 19q.
By immunohistochemical analysis, Suzuki et al. (2002) found that LIG1 expression was downregulated in human psoriatic lesions compared with normal human skin, consistent with findings in Lig1 -/- mice (see ANIMAL MODEL).
Soza et al. (2009) reported that LIG1 is progressively phosphorylated on 4 serines within the N-terminal regulatory domain in a precise temporal order during the cell cycle, with hyperphosphorylation of LIG1 in M phase. They found that replacement of the 4 serines with phosphomimetic aspartic acid impaired association of LIG1 with replication factors in transfected COS-7 cells. It also altered cell morphology and organization of the cytoskeleton.
Human LIG1 joins Okazaki fragments during DNA replication and completes excision repair via interaction with RFC (see 102579). Peng et al. (2012) found that phosphorylation of LIG1 at ser51 regulated interaction between LIG1 and RFC. LIG1 with phosphomimetic asp51, but not with nonphosphorylatable ala51, proved defective in binding purified RFC, increased spontaneous DNA damage and phosphorylation of CHK2 (CHEK2; 604373), and caused cellular senescence.
Crystal Structure
Pascal et al. (2004) reported the crystal structure of human DNA ligase I (residues 233-919) in complex with a nicked, 5-prime adenylated DNA intermediate. The structure shows that the enzyme redirects the path of the double helix to expose the nick termini for the strand-joining reaction. It also reveals a unique feature of mammalian ligases: a DNA-binding domain that allows ligase I to encircle its DNA substrate, stabilizes the DNA in a distorted structure, and positions the catalytic core on the nick. Pascal et al. (2004) suggested that similarities in the toroidal shape and dimensions of DNA ligase I and the proliferating cell nuclear antigen sliding clamp are suggestive of an extensive protein-protein interface that may coordinate the joining of Okazaki fragments.
In a cell line, called 46BR, derived from a girl with immunodeficiency-96 (IMD96; 619774) originally reported by Webster et al. (1982), Barnes et al. (1992) identified compound heterozygous missense mutations in the LIG1 gene (E566K, 126391.0001 and R771W, 126391.0002). The cultured fibroblasts exhibited retarded joining of Okazaki fragments during DNA replication and hypersensitivity to a variety of DNA-damaging agents. In vitro studies showed that the E566K mutation inactivated the enzyme, likely due to its proximity to the catalytic lys568 residue. The patient displayed immunodeficiency, stunted growth, and sun sensitivity; she died of lymphoma at age 19 years. By screening the coding sequence of the LIG1 gene in 4 cases of Bloom syndrome, Barnes et al. (1992) found no mutation.
In 5 patients from 3 unrelated families with IMD96, Maffucci et al. (2018) identified homozygous or compound heterozygous mutations in the LIG1 gene (126391.0002-126391.0004). The mutations, which were found by exome sequencing, segregated with the disorder in the family. All were present at very low frequencies in the ExAC database. In vitro functional expression studies showed that LIG1-null HEK293T cells had loss of viability when exposed to DNA damage, which could be rescued by expression of wildtype LIG1. Cells transfected with the R641L (126391.0004) and R771W (126391.0002) mutations showed intermediate loss of viability when exposed to DNA damage, whereas cells transfected with the frameshift mutation (c.1244delC; 126391.0003) were similar to LIG1-null cells. The findings indicated that absence of LIG1 is associated with disruption of normal DNA repair responses in these cells. Additional in vitro studies showed that the mutations had variably impaired LIG1 catalytic activity: 4.5% for R771W, 7% for R641L, and complete loss of enzyme activity for the frameshift mutation and for E566K, which disrupts an AMP-binding site. The decreased enzyme activity resulted in premature release of unligated adenylated DNA. Patient-derived B and T cells also showed a decreased capacity to respond to chemical and radiation-induced DNA damage. Of note, the R771W and R641L mutant enzyme showed sensitivity to Mg(2+) levels such that increasing Mg(2+) partially restored efficient ligation in vitro. Overall, the findings implicated impaired DNA ligase function in the pathogenesis of the disease.
Although it had been reported that DNA ligase I is essential for cell viability, Bentley et al. (1996) showed that cells lacking DNA ligase I were, in fact, viable. Using gene targeting in embryonic stem (ES) cells, they produced DNA ligase I-deficient mice. Embryos developed normally to midterm, when hematopoiesis usually switches to the fetal liver. Thereupon, acute anemia developed, despite the presence of erythroid-committed progenitor cells in the liver, and the embryos succumbed. Thus, Bentley et al. (1996) concluded that DNA ligase I is required for normal development but is not essential for replication. They proposed that a previously unsuspected redundancy must exist between mammalian DNA ligases.
Bentley et al. (2002) found that injection of Lig1 -/- hematopoietic cells rescued wildtype mice that were lethally irradiated, although rescued animals were anemic, with macrocytosis and reticulocytosis. In culture, Lig1 -/- mouse embryonic fibroblasts (MEFs) proliferated more slowly than wildtype and accumulated DNA replication intermediates. However, Lig1 -/- MEFs showed normal sister chromatid exchange and nucleotide excision repair, as well as repair of DNA damage caused by alkylation and ionizing radiation.
Suzuki et al. (2002) found that Lig1 -/- mice were born at the expected mendelian ratio and exhibited normal growth, behavior, and fertility. However, at the postnatal age of 3 weeks to 4 months, Lig1 -/- mice developed psoriasiform epidermal changes to the tail and facial area, but not the trunk. The epidermal changes were reversed by treatment with common antipsoriatic drugs.
Using gene targeting, Harrison et al. (2002) created mice homozygous for the R771W substitution (126391.0002) found in 1 allele of patient 46BR. Homozygous R771W mice developed normally and were overtly healthy. From 5 weeks of age, they grew more slowly than wildtype, although they eventually achieved normal mature body weight. As young animals, R771W mice had enlarged spleen, with elevated frequency of S-phase cells and increased frequency of immature reticulocytes released prematurely into the circulation. These phenotypes resolved by 5 weeks of age. DNA replication failure was occasionally found in mutant bone marrow. With age, R771W mice showed increased incidence of spontaneous and diverse epithelial tumors, including rare cutaneous adnexal tumors.
In a cell line, called 46BR, derived from a girl with immunodeficiency-96 (IMD96; 619774) originally reported by Webster et al. (1982), Barnes et al. (1992) identified compound heterozygous missense mutations in the LIG1 gene: a glu566-to-lys (E566K) substitution presumably derived from the deceased father and an arg771-to-trp substitution (R771W; 126391.0002) that was inherited from the unaffected mother. The cultured fibroblasts exhibited retarded joining of Okazaki fragments during DNA replication and hypersensitivity to a variety of DNA-damaging agents. Barnes et al. (1992) reported that E566 is highly conserved between human LIG1 and microbial DNA ligases. They found that the E566K mutation inactivated the enzyme, likely due to its proximity to the catalytic lys568 residue. The patient displayed immunodeficiency, stunted growth, and sun sensitivity; she died of lymphoma at age 19 years.
Maffucci et al. (2018) noted that the E566K variant has not been reported in public databases and abolishes enzyme activity.
For discussion of the arg771-to-trp (R771W) substitution in the LIG1 gene that was found in compound heterozygous state in a patient with immunodeficiency-96 (IMD96; 619774) by Barnes et al. (1992), see 126391.0001.
By DNA sequencing, Barnes et al. (1992) determined that SV40-transformed cells derived from 46BR fibroblasts, called 46BR.1G1 cells, lost the inactivating E566K mutation and were homozygous or hemizygous for the R771W mutation. 46BR.1G1 cells grew more vigorously than the primary parental 46BR cell line. However, the amount of LIG1-adenylate intermediate formed by 46BR.1G1 fibroblasts in the presence of ATP was reduced compared with SV40-transformed normal human fibroblasts.
Soza et al. (2009) found that 46BR.1G1 cells showed a defect in maturation of DNA replicative intermediates and accumulated single-stranded and double-stranded DNA breaks. This process was accompanied by phosphorylation of H2AX (H2AFX; 601772) histone and formation of foci of phosphorylated H2AX that marked damaged DNA. However, 46BR.1G1 cells did not activate the S-phase checkpoint, thus entering a new cell cycle with broken DNA and only moderately delayed cell cycle progression.
In 3 members of a consanguineous Sudanese family (kindred C) with IMD96, Maffucci et al. (2018) identified a homozygous c.2311C-T transition in the LIG1 gene, resulting in an arg771-to-trp (R771W) substitution at a highly conserved residue. Familial segregation studies were not performed. The variant was found at a low frequency in the ExAC database (5 x 10(-5)). In vitro functional expression studies in cells transfected with the mutation showed that it significantly impaired LIG1 ligase activity to 4.5% of wildtype. This was associated with increased cellular susceptibility to DNA damage and poor DNA damage response. The R771W mutant had a decreased affinity for Mg(2+) and caused a buildup of unligated adenylated DNA at low Mg(2+) concentrations, indicating abortive ligation. This defect could be partially rescued in vitro by increasing the Mg(2+) concentration. The patients had onset of recurrent, mainly viral, respiratory infections in childhood associated with hypogammaglobulinemia, lymphopenia, red cell macrocytosis, and anemia. Two underwent hematopoietic stem cell transplant. Affected members of the family also carried a homozygous P529L variant in the LIG1 gene that was not present in the ExAC database, but functional studies showed that the variant enzyme behaved similar to wildtype, suggesting that the phenotype is due to the R771W mutation.
In 2 unrelated Caucasian patients (P1 from kindred A and P2 from kindred B) with immunodeficiency-96 (IMD96; 619774), Maffucci et al. (2018) identified compound heterozygous mutations in the LIG1 gene: a 1-bp deletion (c.1244delC), resulting in a frameshift and premature termination (Thr415MetfsTer10), and a c.1922G-T transversion, resulting in an arg641-to-leu (R641L; 126391.0004) substitution at a highly conserved residue. The mutations, which were found by whole-exome sequencing, segregated with the disorder in the families. Although the variants were the same in both patients, haplotype analysis indicated that it was not a founder effect, but rather that the mutations occurred independently. Both mutations were found at low frequencies in the ExAC database (4.2 x 10(-5) for the frameshift and 1.7 x 10(-5) for R641L). In vitro functional expression studies in patient cells and HEK293T cells transfected with the mutations showed that the frameshift resulted in low levels of a truncated protein and absence of catalytic activity, consistent with a complete loss of function. THe R641L variant was expressed at normal levels, but had only 7% of wildtype activity, consistent with a hypomorphic allele. Cells transfected with the R641L mutation showed an intermediate loss of cell viability in response to DNA damage compared to controls. Of note, the R641L mutant enzyme showed sensitivity to Mg(2+) levels such that increasing Mg(2+) partially restored efficient ligation. Patient-derived B and T cells showed impaired DNA repair capacity in response to chemical- and radiation-induced damage. There was also some evidence of decreased IgH rearrangement and somatic hypermutation. Overall, the findings implicated impaired DNA ligase function in the pathogenesis of the disease. The patients had onset of recurrent, mainly viral, respiratory infections in early childhood associated with hypogammaglobulinemia, lymphopenia, red cell macrocytosis, and NK cell deficiency. They were treated with Ig replacement.
For discussion of the c.1922G-T transversion in the LIG1 gene, resulting in an arg641-to-leu (R641L) substitution, that was found in compound heterozygous state in 2 unrelated patients with immunodeficiency-96 (IMD96; 619774) by Maffucci et al. (2018), see 126391.0003.
Barnes, D. E., Johnston, L. H., Kodama, K., Tomkinson, A. E., Lasko, D. D., Lindahl, T. Human DNA ligase I cDNA: cloning and functional expression in Saccharomyces cerevisiae. Proc. Nat. Acad. Sci. 87: 6679-6683, 1990. [PubMed: 2204063] [Full Text: https://doi.org/10.1073/pnas.87.17.6679]
Barnes, D. E., Kodama, K.-I., Tynan, K., Trask, B. J., Christensen, M., de Jong, P. J., Spurr, N. K., Lindahl, T., Mohrenweiser, H. W. Assignment of the gene-encoding DNA ligase I to human chromosome 19q13.2-13.3. Genomics 12: 164-166, 1992. [PubMed: 1733856] [Full Text: https://doi.org/10.1016/0888-7543(92)90422-o]
Barnes, D. E., Tomkinson, A. E., Lehmann, A. R., Webster, A. D. B., Lindahl, T. Mutations in the DNA ligase I gene of an individual with immunodeficiencies and cellular hypersensitivity to DNA-damaging agents. Cell 69: 495-503, 1992. [PubMed: 1581963] [Full Text: https://doi.org/10.1016/0092-8674(92)90450-q]
Bentley, D. J., Harrison, C., Ketchen, A.-M., Redhead, N. J., Samuel, K., Waterfall, M., Ansell, J. D., Melton, D. W. DNA ligase I null mouse cells show normal DNA repair activity but altered DNA replication and reduced genome stability. J. Cell Sci. 115: 1551-1561, 2002. [PubMed: 11896201] [Full Text: https://doi.org/10.1242/jcs.115.7.1551]
Bentley, D. J., Selfridge, J., Millar, J. K., Samuel, K., Hole, N., Ansell, J. D., Melton, D. W. DNA ligase I is required for fetal liver erythropoiesis but is not essential for mammalian cell viability. Nature Genet. 13: 489-491, 1996. [PubMed: 8696349] [Full Text: https://doi.org/10.1038/ng0896-489]
Gariboldi, M., Montecucco, A., Columbano, A., Ledda-Columbano, G. M., Savini, E., Manenti, G., Pierotti, M. A., Dragani, T. A. Genetic mapping and expression analysis of the murine DNA ligase gene. Molec. Carcinogen. 14: 71-74, 1995. [PubMed: 7576101] [Full Text: https://doi.org/10.1002/mc.2940140202]
Harrison, C., Ketchen, A.-M., Redhead, N. J., O'Sullivan, M. J., Melton, D. W. Replication failure, genome instability, and increased cancer susceptibility in mice with a point mutation in the DNA ligase I gene. Cancer Res. 62: 4065-4074, 2002. [PubMed: 12124343]
Lindahl, T., Barnes, D. E. Mammalian DNA ligases. Annu. Rev. Biochem. 61: 251-281, 1992. [PubMed: 1497311] [Full Text: https://doi.org/10.1146/annurev.bi.61.070192.001343]
Maffucci, P., Chavez, J., Jurkiw, T. J., O'Brien, P. J., Abbott, J. K., Reynolds, P. R., Worth, A., Notarangelo, L. D., Felgentreff, K., Cortes, P., Boisson, B., Radigan, L., Cobat, A., Dinakar, C., Ehlayel, M., Ben-Omran, T., Gelfand, E. W., Casanova, J.-L., Cunningham-Rundles, C. Biallelic mutations in DNA ligase 1 underlie a spectrum of immune deficiencies. J. Clin. Invest. 128: 5489-5504, 2018. [PubMed: 30395541] [Full Text: https://doi.org/10.1172/JCI99629]
Noguiez, P., Barnes, D. E., Mohrenweiser, H. W., Lindahl, T. Structure of the human DNA ligase I gene. Nucleic Acids Res. 20: 3845-3850, 1992. [PubMed: 1508669] [Full Text: https://doi.org/10.1093/nar/20.15.3845]
Pascal, J. M., O'Brien, P. J., Tomkinson, A. E., Ellenberger, T. Human DNA ligase I completely encircles and partially unwinds nicked DNA. Nature 432: 473-478, 2004. [PubMed: 15565146] [Full Text: https://doi.org/10.1038/nature03082]
Peng, Z., Liao, Z., Dziegielewska, B., Matsumoto, Y., Thomas, S., Wan, Y., Yang, A., Tomkinson, A. E. Phosphorylation of serine 51 regulates the interaction of human DNA ligase I with replication factor C and its participation in DNA replication and repair. J. Biol. Chem. 287: 36711-36719, 2012. [PubMed: 22952233] [Full Text: https://doi.org/10.1074/jbc.M112.383570]
Soza, S., Leva, V., Vago, R., Ferrari, G., Mazzini, G., Biamonti, G., Montecucco, A. DNA ligase I deficiency leads to replication-dependent DNA damage and impacts cell morphology without blocking cell cycle progression. Molec. Cell. Biol. 29: 2032-2041, 2009. [PubMed: 19223467] [Full Text: https://doi.org/10.1128/MCB.01730-08]
Suzuki, Y., Miura, H., Tanemura, A., Kobayashi, K., Kondoh, G., Sano, S., Ozawa, K., Inui, S., Nakata, A., Takagi, T., Tohyama, M., Yoshikawa, K., Itami, S. Targeted disruption of LIG-1 gene results in psoriasiform epidermal hyperplasia. FEBS Lett. 521: 67-71, 2002. [PubMed: 12067728] [Full Text: https://doi.org/10.1016/s0014-5793(02)02824-7]
Trask, B., Fertitta, A., Christensen, M., Youngblom, J., Bergmann, A., Copeland, A., de Jong, P., Mohrenweiser, H., Olsen, A., Carrano, A., Tynan, K. Fluorescence in situ hybridization mapping of human chromosome 19: cytogenetic band location of 540 cosmids and 70 genes or DNA markers. Genomics 15: 133-145, 1993. [PubMed: 8432525] [Full Text: https://doi.org/10.1006/geno.1993.1021]
Webster, D., Arlett, C. F., Harcourt, S. A., Teo, I., Henderson, L. A new syndrome of immunodeficiency and increased cellular sensitivity to DNA damaging agents.In: Bridges, B. A.; Harnden, D. G. : Ataxia-telangiectasia: A Cellular and Molecular Link between Cancer, Neuropathology, and Immune Deficiency. New York: John Wiley (pub.) 1982. Pp. 379-386.