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Journal articles on the topic 'Ligase IV'

Author: Grafiati

Published: 4 June 2021

Last updated: 6 September 2023

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1

Nick McElhinny, Stephanie A., Carey M. Snowden, Joseph McCarville, and Dale A. Ramsden. "Ku Recruits the XRCC4-Ligase IV Complex to DNA Ends." Molecular and Cellular Biology 20, no. 9 (May 1, 2000): 2996–3003. http://dx.doi.org/10.1128/mcb.20.9.2996-3003.2000.

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ABSTRACT Genetic experiments have determined that Ku, XRCC4, and ligase IV are required for repair of double-strand breaks by the end-joining pathway. The last two factors form a tight complex in cells. However, ligase IV is only one of three known mammalian ligases and is intrinsically the least active in intermolecular ligation; thus, the biochemical basis for requiring this ligase has been unclear. We demonstrate here a direct physical interaction between the XRCC4-ligase IV complex and Ku. This interaction is stimulated once Ku binds to DNA ends. Since XRCC4-ligase IV alone has very low DNA binding activity, Ku is required for effective recruitment of this ligase to DNA ends. We further show that this recruitment is critical for efficient end-joining activity in vitro. Preformation of a complex containing Ku and XRCC4-ligase IV increases the initial ligation rate 20-fold, indicating that recruitment of the ligase is an important limiting step in intermolecular ligation. Recruitment by Ku also allows XRCC4-ligase IV to use Ku's high affinity for DNA ends to rapidly locate and ligate ends in an excess of unbroken DNA, a necessity for end joining in cells. These properties are conferred only on ligase IV, because Ku does not similarly interact with the other mammalian ligases. We have therefore defined cell-free conditions that reflect the genetic requirement for ligase IV in cellular end joining and consequently can explain in molecular terms why this factor is required.

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2

Malashetty, Vidyasagar, Audrey Au, Jose Chavez, Mary Hanna, Jennifer Chu, Jesse Penna, and Patricia Cortes. "The DNA binding domain and the C-terminal region of DNA Ligase IV specify its role in V(D)J recombination." PLOS ONE 18, no. 2 (February 24, 2023): e0282236. http://dx.doi.org/10.1371/journal.pone.0282236.

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DNA Ligase IV is responsible for the repair of DNA double-strand breaks (DSB), including DSBs that are generated during V(D)J recombination. Like other DNA ligases, Ligase IV contains a catalytic core with three subdomains—the DNA binding (DBD), the nucleotidyltransferase (NTD), and the oligonucleotide/oligosaccharide-fold subdomain (OBD). Ligase IV also has a unique C-terminal region that includes two BRCT domains, a nuclear localization signal sequence and a stretch of amino acid that participate in its interaction with XRCC4. Out of the three mammalian ligases, Ligase IV is the only ligase that participates in and is required for V(D)J recombination. Identification of the minimal domains within DNA Ligase IV that contribute to V(D)J recombination has remained unresolved. The interaction of the Ligase IV DNA binding domain with Artemis, and the interaction of its C-terminal region with XRCC4, suggest that both of these regions that also interact with the Ku70/80 heterodimer are important and might be sufficient for mediating participation of DNA Ligase IV in V(D)J recombination. This hypothesis was investigated by generating chimeric ligase proteins by swapping domains, and testing their ability to rescue V(D)J recombination in Ligase IV-deficient cells. We demonstrate that a fusion protein containing Ligase I NTD and OBDs flanked by DNA Ligase IV DBD and C-terminal region is sufficient to support V(D)J recombination. This chimeric protein, which we named Ligase 37, complemented formation of coding and signal joints. Coding joints generated with Ligase 37 were shorter than those observed with wild type DNA Ligase IV. The shorter length was due to increased nucleotide deletions and decreased nucleotide insertions. Additionally, overexpression of Ligase 37 in a mouse pro-B cell line supported a shift towards shorter coding joints. Our findings demonstrate that the ability of DNA Ligase IV to participate in V(D)J recombination is in large part mediated by its DBD and C-terminal region.

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3

Chistiakov, Dimitry A., Natalia V. Voronova, and Alexander P. Chistiakov. "Ligase IV syndrome." European Journal of Medical Genetics 52, no. 6 (November 2009): 373–78. http://dx.doi.org/10.1016/j.ejmg.2009.05.009.

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4

Wei, Y. F., P. Robins, K. Carter, K. Caldecott, D. J. Pappin, G. L. Yu, R. P. Wang, B. K. Shell, R. A. Nash, and P. Schär. "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." Molecular and Cellular Biology 15, no. 6 (June 1995): 3206–16. http://dx.doi.org/10.1128/mcb.15.6.3206.

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Three distinct DNA ligases, I to III, have been found previously in mammalian cells, but a cloned cDNA has been identified only for DNA ligase I, an essential enzyme active in DNA replication. A short peptide sequence conserved close to the C terminus of all known eukaryotic DNA ligases was used to search for additional homologous sequences in human cDNA libraries. Two different incomplete cDNA clones that showed partial homology to the conserved peptide were identified. Full-length cDNAs were obtained and expressed by in vitro transcription and translation. The 103-kDa product of one cDNA clone formed a characteristic complex with the XRCC1 DNA repair protein and was identical with the previously described DNA ligase III. DNA ligase III appears closely related to the smaller DNA ligase II. The 96-kDa in vitro translation product of the second cDNA clone was also shown to be an ATP-dependent DNA ligase. A fourth DNA ligase (DNA ligase IV) has been purified from human cells and shown to be identical to the 96-kDa DNA ligase by unique agreement between mass spectrometry data on tryptic peptides from the purified enzyme and the predicted open reading frame of the cloned cDNA. The amino acid sequences of DNA ligases III and IV share a related active-site motif and several short regions of homology with DNA ligase I, other DNA ligases, and RNA capping enzymes. DNA ligases III and IV are encoded by distinct genes located on human chromosomes 17q11.2-12 and 13q33-34, respectively.

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5

Zhao, Bailin, Tasmin Naila, Michael R. Lieber, and Alan E. Tomkinson. "NAD+ is not utilized as a co-factor for DNA ligation by human DNA ligase IV." Nucleic Acids Research 48, no. 22 (December 2, 2020): 12746–50. http://dx.doi.org/10.1093/nar/gkaa1118.

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Abstract As nucleotidyl transferases, formation of a covalent enzyme-adenylate intermediate is a common first step of all DNA ligases. While it has been shown that eukaryotic DNA ligases utilize ATP as the adenylation donor, it was recently reported that human DNA ligase IV can also utilize NAD+ and, to a lesser extent ADP-ribose, as the source of the adenylate group and that NAD+, unlike ATP, enhances ligation by supporting multiple catalytic cycles. Since this unexpected finding has significant implications for our understanding of the mechanisms and regulation of DNA double strand break repair, we attempted to confirm that NAD+ and ADP-ribose can be used as co-factors by human DNA ligase IV. Here, we provide evidence that NAD+ does not enhance ligation by pre-adenylated DNA ligase IV, indicating that this co-factor is not utilized for re-adenylation and subsequent cycles of ligation. Moreover, we find that ligation by de-adenylated DNA ligase IV is dependent upon ATP not NAD+ or ADP-ribose. Thus, we conclude that human DNA ligase IV cannot use either NAD+ or ADP-ribose as adenylation donor for ligation.

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6

Rusché, Laura N., Catherine E. Huang, Kenneth J. Piller, Michael Hemann, Elizabeth Wirtz, and Barbara Sollner-Webb. "The Two RNA Ligases of the Trypanosoma brucei RNA Editing Complex: Cloning the Essential Band IV Gene and Identifying the Band V Gene." Molecular and Cellular Biology 21, no. 4 (February 15, 2001): 979–89. http://dx.doi.org/10.1128/mcb.21.4.979-989.2001.

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ABSTRACT Kinetoplastid RNA editing is a posttranscriptional insertion and deletion of U residues in mitochondrial transcripts that involves RNA ligase. A complex of seven different polypeptides purified fromTrypanosoma brucei mitochondria that catalyzes accurate RNA editing contains RNA ligases of ∼57 kDa (band IV) and ∼50 kDa (band V). From a partial amino acid sequence, cDNA and genomic clones of band IV were isolated, making it the first cloned component of the minimal RNA editing complex. It is indeed an RNA ligase, for when expressed inEscherichia coli, the protein autoadenylylates and catalyzes RNA joining. Overexpression studies revealed that T. brucei can regulate of total band IV protein at the level of translation or protein stability, even upon massively increased mRNA levels. The protein's mitochondrial targeting was confirmed by its location, size when expressed in T. brucei and E. coli, and N-terminal sequence. Importantly, genetic knockout studies demonstrated that the gene for band IV is essential in procyclic trypanosomes. The band IV and band V RNA ligases of the RNA editing complex therefore serve different functions. We also identified the gene for band V RNA ligase, a protein much more homologous to band IV than to other known ligases.

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7

Tomkinson, Alan E., Tasmin Naila, and Seema Khattri Bhandari. "Altered DNA ligase activity in human disease." Mutagenesis 35, no. 1 (October 20, 2019): 51–60. http://dx.doi.org/10.1093/mutage/gez026.

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Abstract The joining of interruptions in the phosphodiester backbone of DNA is critical to maintain genome stability. These breaks, which are generated as part of normal DNA transactions, such as DNA replication, V(D)J recombination and meiotic recombination as well as directly by DNA damage or due to DNA damage removal, are ultimately sealed by one of three human DNA ligases. DNA ligases I, III and IV each function in the nucleus whereas DNA ligase III is the sole enzyme in mitochondria. While the identification of specific protein partners and the phenotypes caused either by genetic or chemical inactivation have provided insights into the cellular functions of the DNA ligases and evidence for significant functional overlap in nuclear DNA replication and repair, different results have been obtained with mouse and human cells, indicating species-specific differences in the relative contributions of the DNA ligases. Inherited mutations in the human LIG1 and LIG4 genes that result in the generation of polypeptides with partial activity have been identified as the causative factors in rare DNA ligase deficiency syndromes that share a common clinical symptom, immunodeficiency. In the case of DNA ligase IV, the immunodeficiency is due to a defect in V(D)J recombination whereas the cause of the immunodeficiency due to DNA ligase I deficiency is not known. Overexpression of each of the DNA ligases has been observed in cancers. For DNA ligase I, this reflects increased proliferation. Elevated levels of DNA ligase III indicate an increased dependence on an alternative non-homologous end-joining pathway for the repair of DNA double-strand breaks whereas elevated level of DNA ligase IV confer radioresistance due to increased repair of DNA double-strand breaks by the major non-homologous end-joining pathway. Efforts to determine the potential of DNA ligase inhibitors as cancer therapeutics are on-going in preclinical cancer models.

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8

Przewloka, Marcin R., Paige E. Pardington, Steven M. Yannone, David J. Chen, and Robert B. Cary. "In Vitro and In Vivo Interactions of DNA Ligase IV with a Subunit of the Condensin Complex." Molecular Biology of the Cell 14, no. 2 (February 2003): 685–97. http://dx.doi.org/10.1091/mbc.e01-11-0117.

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Several findings have revealed a likely role for DNA ligase IV, and interacting protein XRCC4, in the final steps of mammalian DNA double-strand break repair. Recent evidence suggests that the human DNA ligase IV protein plays a critical role in the maintenance of genomic stability. To identify protein–protein interactions that may shed further light on the molecular mechanisms of DSB repair and the biological roles of human DNA ligase IV, we have used the yeast two-hybrid system in conjunction with traditional biochemical methods. These efforts have resulted in the identification of a physical association between the DNA ligase IV polypeptide and the human condensin subunit known as hCAP-E. The hCAP-E polypeptide, a member of the Structural Maintenance of Chromosomes (SMC) super-family of proteins, coimmunoprecipitates from cell extracts with DNA ligase IV. Immunofluorescence studies reveal colocalization of DNA ligase IV and hCAP-E in the interphase nucleus, whereas mitotic cells display colocalization of both polypeptides on mitotic chromosomes. Strikingly, the XRCC4 protein is excluded from the area of mitotic chromosomes, suggesting the formation of specialized DNA ligase IV complexes subject to cell cycle regulation. We discuss our findings in light of known and hypothesized roles for ligase IV and the condensin complex.

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9

Wang, Yu, Brandon J. Lamarche, and Ming-Daw Tsai. "Human DNA Ligase IV and the Ligase IV/XRCC4 Complex: Analysis of Nick Ligation Fidelity†." Biochemistry 46, no. 17 (May 2007): 4962–76. http://dx.doi.org/10.1021/bi0621516.

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10

Liu, Sicheng, Xunyue Liu, Radhika Pankaj Kamdar, Rujira Wanotayan, Mukesh Kumar Sharma, Noritaka Adachi, and Yoshihisa Matsumoto. "C-terminal region of DNA ligase IV drives XRCC4/DNA ligase IV complex to chromatin." Biochemical and Biophysical Research Communications 439, no. 2 (September 2013): 173–78. http://dx.doi.org/10.1016/j.bbrc.2013.08.068.

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11

Malu, Shruti, Pablo De Ioannes, Mikhail Kozlov, Marsha Greene, Dailia Francis, Mary Hanna, Jesse Pena, et al. "Artemis C-terminal region facilitates V(D)J recombination through its interactions with DNA Ligase IV and DNA-PKcs." Journal of Experimental Medicine 209, no. 5 (April 23, 2012): 955–63. http://dx.doi.org/10.1084/jem.20111437.

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Artemis is an endonuclease that opens coding hairpin ends during V(D)J recombination and has critical roles in postirradiation cell survival. A direct role for the C-terminal region of Artemis in V(D)J recombination has not been defined, despite the presence of immunodeficiency and lymphoma development in patients with deletions in this region. Here, we report that the Artemis C-terminal region directly interacts with the DNA-binding domain of Ligase IV, a DNA Ligase which plays essential roles in DNA repair and V(D)J recombination. The Artemis–Ligase IV interaction is specific and occurs independently of the presence of DNA and DNA–protein kinase catalytic subunit (DNA-PKcs), another protein known to interact with the Artemis C-terminal region. Point mutations in Artemis that disrupt its interaction with Ligase IV or DNA-PKcs reduce V(D)J recombination, and Artemis mutations that affect interactions with Ligase IV and DNA-PKcs show additive detrimental effects on coding joint formation. Signal joint formation remains unaffected. Our data reveal that the C-terminal region of Artemis influences V(D)J recombination through its interaction with both Ligase IV and DNA-PKcs.

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12

Wu, Peï-Yu, Philippe Frit, SriLakshmi Meesala, Stéphanie Dauvillier, Mauro Modesti, Sara N. Andres, Ying Huang, et al. "Structural and Functional Interaction between the Human DNA Repair Proteins DNA Ligase IV and XRCC4." Molecular and Cellular Biology 29, no. 11 (March 30, 2009): 3163–72. http://dx.doi.org/10.1128/mcb.01895-08.

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ABSTRACT Nonhomologous end-joining represents the major pathway used by human cells to repair DNA double-strand breaks. It relies on the XRCC4/DNA ligase IV complex to reseal DNA strands. Here we report the high-resolution crystal structure of human XRCC4 bound to the carboxy-terminal tandem BRCT repeat of DNA ligase IV. The structure differs from the homologous Saccharomyces cerevisiae complex and reveals an extensive DNA ligase IV binding interface formed by a helix-loop-helix structure within the inter-BRCT linker region, as well as significant interactions involving the second BRCT domain, which induces a kink in the tail region of XRCC4. We further demonstrate that interaction with the second BRCT domain of DNA ligase IV is necessary for stable binding to XRCC4 in cells, as well as to achieve efficient dominant-negative effects resulting in radiosensitization after ectopic overexpression of DNA ligase IV fragments in human fibroblasts. Together our findings provide unanticipated insight for understanding the physical and functional architecture of the nonhomologous end-joining ligation complex.

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13

Namekawa, Satoshi, Yosuke Ichijima, Fumika Hamada, Nobuyuki Kasai, Kazuki Iwabata, Takayuki Nara, Hirobumi Teraoka, Fumio Sugawara, and Kengo Sakaguchi. "DNA ligase IV from a basidiomycete, Coprinus cinereus, and its expression during meiosis." Microbiology 149, no. 8 (August 1, 2003): 2119–28. http://dx.doi.org/10.1099/mic.0.26311-0.

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DNA ligase IV is thought to be involved in DNA double-strand break repair and DNA non-homologous end-joining pathways, but these mechanisms are still unclear. To investigate the roles of DNA ligase IV from a biologically functional viewpoint, the authors studied its relationship to meiosis in a basidiomycete, Coprinus cinereus, which shows a highly synchronous meiotic cell cycle. The C. cinereus cDNA homologue of DNA ligase IV (CcLIG4) was successfully cloned. The 3·2 kb clone including the ORF encoded a predicted product of 1025 amino acid residues with a molecular mass of 117 kDa. A specific inserted sequence composed of 95 amino acids rich in aspartic acid and glutamic acid could be detected between tandem BRCT domains. The inserted sequence had no sequence identity with other eukaryotic counterparts of DNA ligase IV or with another aspartic acid and glutamic acid rich sequence inserted in C. cinereus proliferating cell nuclear antigen (CcPCNA), although the length and the percentages of aspartic and glutamic acids were similar. In addition, the recombinant CcLIG4 protein not only showed ATP-dependent ligase activity, but also used (dT)16/poly(dA) and (dT)16/poly(rA) as substrates, and had double-strand ligation activity, like human DNA ligase IV. Northern hybridization analysis and in situ hybridization indicated that CcLIG4 was expressed not only at the pre-meiotic S phase but also at meiotic prophase I. Intense signals were observed in leptotene and zygotene. Based on these observations, the possible role(s) of C. cinereus DNA ligase IV during meiosis are discussed.

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14

Robins, Peter, and Tomas Lindahl. "DNA Ligase IV from HeLa Cell Nuclei." Journal of Biological Chemistry 271, no. 39 (September 27, 1996): 24257–61. http://dx.doi.org/10.1074/jbc.271.39.24257.

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15

Francis, Dailia B., Mikhail Kozlov, Jose Chavez, Jennifer Chu, Shruti Malu, Mary Hanna, and Patricia Cortes. "DNA Ligase IV regulates XRCC4 nuclear localization." DNA Repair 21 (September 2014): 36–42. http://dx.doi.org/10.1016/j.dnarep.2014.05.010.

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16

Stiff, Thomas, Emma Shtivelman, Penny Jeggo, and Boris Kysela. "AHNAK interacts with the DNA ligase IV–XRCC4 complex and stimulates DNA ligase IV-mediated double-stranded ligation." DNA Repair 3, no. 3 (March 4, 2004): 245–56. http://dx.doi.org/10.1016/j.dnarep.2003.11.001.

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17

O'Hearn, Sean F., Catherine E. Huang, Mike Hemann, Alevtina Zhelonkina, and Barbara Sollner-Webb. "Trypanosoma brucei RNA Editing Complex." Molecular and Cellular Biology 23, no. 21 (November 1, 2003): 7909–19. http://dx.doi.org/10.1128/mcb.23.21.7909-7919.2003.

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ABSTRACT Maturation of Trypanosoma brucei mitochondrial mRNA involves massive posttranscriptional insertion and deletion of uridine residues. This RNA editing utilizes an enzymatic complex with seven major proteins, band I through band VII. We here use RNA interference (RNAi) to examine the band II and band V proteins. Band II is found essential for viability; it is needed to maintain the normal structure of the editing complex and to retain the band V ligase protein. Previously, band III was found essential for certain activities, including maintenance of the editing complex and retention of the band IV ligase protein. Thus, band II and band V form a protein pair with features analogous to the band III/band IV ligase pair. Since band V is specific for U insertion and since band IV is needed for U deletion, their parallel organization suggests that the editing complex has a pseudosymmetry. However, unlike the essential band IV ligase, RNAi to band V has only a morphological but no growth rate effect, suggesting that it is stimulatory but nonessential. Indeed, in vitro analysis of band V RNAi cell extract demonstrates that band IV can seal U insertion when band V is lacking. Thus, band IV ligase is the first activity of the basic editing complex shown able to serve in both forms of editing. Our studies also indicate that the U insertional portion may be less central in the editing complex than the corresponding U deletional portion.

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18

Gu, Jiafeng, Haihui Lu, Brigette Tippin, Noriko Shimazaki, Myron F. Goodman, and Michael R. Lieber. "XRCC4:DNA ligase IV can ligate incompatible DNA ends and can ligate across gaps." EMBO Journal 26, no. 4 (February 8, 2007): 1010–23. http://dx.doi.org/10.1038/sj.emboj.7601559.

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19

Gu, Jiafeng, Haihui Lu, Brigette Tippin, Noriko Shimazaki, Myron F. Goodman, and Michael R. Lieber. "XRCC4:DNA ligase IV can ligate incompatible DNA ends and can ligate across gaps." EMBO Journal 26, no. 14 (July 25, 2007): 3506–7. http://dx.doi.org/10.1038/sj.emboj.7601729.

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20

Mahajan, Kiran N., Stephanie A. Nick McElhinny, Beverly S. Mitchell, and Dale A. Ramsden. "Association of DNA Polymerase μ (pol μ) with Ku and Ligase IV: Role for pol μ in End-Joining Double-Strand Break Repair." Molecular and Cellular Biology 22, no. 14 (July 15, 2002): 5194–202. http://dx.doi.org/10.1128/mcb.22.14.5194-5202.2002.

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ABSTRACT Mammalian DNA polymerase μ (pol μ) is related to terminal deoxynucleotidyl transferase, but its biological role is not yet clear. We show here that after exposure of cells to ionizing radiation (IR), levels of pol μ protein increase. pol μ also forms discrete nuclear foci after IR, and these foci are largely coincident with IR-induced foci of γH2AX, a previously characterized marker of sites of DNA double-strand breaks. pol μ is thus part of the cellular response to DNA double-strand breaks. pol μ also associates in cell extracts with the nonhomologous end-joining repair factor Ku and requires both Ku and another end-joining factor, XRCC4-ligase IV, to form a stable complex on DNA in vitro. pol μ in turn facilitates both stable recruitment of XRCC4-ligase IV to Ku-bound DNA and ligase IV-dependent end joining. In contrast, the related mammalian DNA polymerase β does not form a complex with Ku and XRCC4-ligase IV and is less effective than pol μ in facilitating joining mediated by these factors. Our data thus support an important role for pol μ in the end-joining pathway for repair of double-strand breaks.

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21

Berg, Elke, Morten O. Christensen, Ilaria Dalla Rosa, Ellen Wannagat, Reiner U. Jänicke, Lennart M. Rösner, Wilhelm G. Dirks, Fritz Boege, and Christian Mielke. "XRCC4 controls nuclear import and distribution of Ligase IV and exchanges faster at damaged DNA in complex with Ligase IV." DNA Repair 10, no. 12 (December 2011): 1232–42. http://dx.doi.org/10.1016/j.dnarep.2011.09.012.

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22

Marchetti, Caterina, Sarah A. Walker, Federico Odreman, Alessandro Vindigni, Aidan J. Doherty, and Penny Jeggo. "Identification of a novel motif in DNA ligases exemplified by DNA ligase IV." DNA Repair 5, no. 7 (July 2006): 788–98. http://dx.doi.org/10.1016/j.dnarep.2006.03.011.

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23

Baker, Amy, Kent J. Rohleder, Les A. Hanakahi, and Gary Ketner. "Adenovirus E4 34k and E1b 55k Oncoproteins Target Host DNA Ligase IV for Proteasomal Degradation." Journal of Virology 81, no. 13 (April 25, 2007): 7034–40. http://dx.doi.org/10.1128/jvi.00029-07.

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ABSTRACT Cells infected by adenovirus E4 mutants accumulate end-to-end concatemers of the viral genome that are assembled from unit-length viral DNAs by nonhomologous end joining (NHEJ). Genome concatenation can be prevented by expression either of E4 11k (product of E4orf3) or of the complex of E4 34k (product of E4orf6) and E1b 55k. Both E4 11k and the E4 34k/E1b 55k complex prevent concatenation at least in part by inactivation of the host protein Mre11: E4 11k sequesters Mre11 in aggresomes, while the E4 34k/E1b 55k complex participates in a virus-specific E3 ubiquitin ligase that mediates ubiquitination and proteasomal degradation. The E4 34k/E1b 55k complex, but not E4 11k, also inhibits NHEJ activity on internal breaks in the viral genome and on V(D)J recombination substrate plasmids, suggesting that it may interfere with NHEJ independently of its effect on Mre11. We show here that DNA ligase IV, which performs the joining step of NHEJ, is degraded as a consequence of adenovirus infection. Degradation is dependent upon E4 34k and E1b 55k, functional proteasomes, and the activity of cellular cullin 5, a component of the adenoviral ubiquitin ligase. DNA ligase IV also interacts physically with E1b 55k. The data demonstrate that DNA ligase IV, like Mre11, is a substrate for the adenovirus-specific E3 ubiquitin ligase; identify an additional viral approach to prevention of genome concatenation; and provide a mechanism for the general inhibition of NHEJ by adenoviruses.

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24

Cruz-Reyes, Jorge, Alevtina G. Zhelonkina, Catherine E. Huang, and Barbara Sollner-Webb. "Distinct Functions of Two RNA Ligases in Active Trypanosoma brucei RNA Editing Complexes." Molecular and Cellular Biology 22, no. 13 (July 1, 2002): 4652–60. http://dx.doi.org/10.1128/mcb.22.13.4652-4660.2002.

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ABSTRACT Trypanosome RNA editing is a unique U insertion and U deletion process that involves cycles of pre-mRNA cleavage, terminal U addition or U removal, and religation. This editing can occur at massive levels and is directed by base pairing of trans-acting guide RNAs. Both U insertion and U deletion cycles are catalyzed by a single protein complex that contains only seven major proteins, band I through band VII. However, little is known about their catalytic functions, except that band IV and band V are RNA ligases and genetic analysis indicates that the former is important in U deletion. Here we establish biochemical approaches to distinguish the individual roles of these ligases, based on their distinctive ATP and pyrophosphate utilization. These in vitro analyses revealed that both ligases serve in RNA editing. Band V is the RNA editing ligase that functions very selectively to seal in U insertion (IREL), while band IV is the RNA editing ligase needed to seal in U deletion (DREL). In combination with our earlier findings about the cleavage and the U-addition/U-removal steps of U deletion and U insertion, these results show that all three steps of these editing pathways exhibit major differences and suggest that the editing complex could have physically separate regions for U deletion and U insertion.

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25

Friesen, Claudia, Miriam Uhl, Ulrich Pannicke, Klaus Schwarz, Erich Miltner, and Klaus-Michael Debatin. "DNA-Ligase IV and DNA-Protein Kinase Play a Critical Role in Deficient Caspases Activation in Apoptosis-resistant Cancer Cells by Using Doxorubicin." Molecular Biology of the Cell 19, no. 8 (August 2008): 3283–89. http://dx.doi.org/10.1091/mbc.e08-03-0306.

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Resistance toward cytotoxic drugs is one of the primary causes for therapeutic failure in cancer therapy. DNA repair mechanisms as well as deficient caspases activation play a critical role in apoptosis resistance of tumor cells toward anticancer drug treatment. Here, we discovered that deficient caspases activation in apoptosis-resistant cancer cells depends on DNA-ligase IV and DNA-protein kinase (DNA-PK), playing crucial roles in the nonhomologous end joining (NHEJ) pathway, which is the predominant pathway for DNA double-strand break repair (DNA-DSB-repair) in mammalian cells. DNA-PK(+/+) as well as DNA-ligase IV (+/+) cancer cells were apoptosis resistant and deficient in activation of caspase-3, caspase-9, and caspase-8 and in cleavage of poly(ADP-ribose) polymerase after doxorubicin treatment. Inhibition of NHEJ by knocking out DNA-PK or DNA-ligase IV restored caspases activation and apoptosis sensitivity after doxorubicin treatment. In addition, inhibition of caspases activation prevented doxorubicin-induced apoptosis but could not prevent doxorubicin-induced DNA damage, indicating that induction of DNA damage is independent of caspases activation. However, caspases activation depends on induction of DNA damage left unrepaired by NHEJ-DNA-DSB-repair. We conclude that DNA damage left unrepaired by DNA-ligase IV or DNA-PK might be the initiator for caspases activation by doxorubicin in cancer cells. Failure in caspases activation using doxorubicin depends on loss of DNA damage and is due to higher rates of NHEJ-DNA-DBS-repair.

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26

Hsu, Hsin-Ling, Steven M. Yannone, and David J. Chen. "Defining interactions between DNA-PK and ligase IV/XRCC4." DNA Repair 1, no. 3 (March 2002): 225–35. http://dx.doi.org/10.1016/s1568-7864(01)00018-0.

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27

Gerasimou, Petroula, Laura Koumas, Andri Miltiadous, Ioannis Kyprianou, Jianxiang Chi, Rafaella Gavrielidou, Elena Socratous, et al. "The rare DNA ligase IV syndrome: A case report." Human Pathology: Case Reports 22 (November 2020): 200442. http://dx.doi.org/10.1016/j.ehpc.2020.200442.

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Jiang, Jinqiu, Wenjing Tang, Yunfei An, Maozhi Tang, Junfeng Wu, Tao Qin, and Xiaodong Zhao. "Molecular and immunological characterization of DNA ligase IV deficiency." Clinical Immunology 163 (February 2016): 75–83. http://dx.doi.org/10.1016/j.clim.2015.12.016.

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29

Gatz, S. A., L. Ju, R. Gruber, E. Hoffmann, A. M. Carr, Z. Q. Wang, C. Liu, and P. A. Jeggo. "Requirement for DNA Ligase IV during Embryonic Neuronal Development." Journal of Neuroscience 31, no. 27 (July 6, 2011): 10088–100. http://dx.doi.org/10.1523/jneurosci.1324-11.2011.

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30

Gilson, Timra, Amy E. Greer, Alessandro Vindigni, Gary Ketner, and Leslyn A. Hanakahi. "The α2 helix in the DNA ligase IV BRCT-1 domain is required for targeted degradation of ligase IV during adenovirus infection." Virology 428, no. 2 (July 2012): 128–35. http://dx.doi.org/10.1016/j.virol.2012.03.006.

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31

Huang, Catherine E., Sean F. O'Hearn, and Barbara Sollner-Webb. "Assembly and Function of the RNA Editing Complex in Trypanosoma brucei Requires Band III Protein." Molecular and Cellular Biology 22, no. 9 (May 1, 2002): 3194–203. http://dx.doi.org/10.1128/mcb.22.9.3194-3203.2002.

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ABSTRACT Trypanosome RNA editing, the posttranscriptional insertion and deletion of U residues in mitochondrial transcripts, is catalyzed by a protein complex containing seven distinct proteins. In this study, we cloned the gene for band III, a 555-amino-acid protein with two separate zinc finger motifs. We prepared antibodies that showed band III protein cofractionates with the previously characterized band IV protein throughout the purification of the editing complex and is not found free or in other protein associations; therefore, it is a true constituent of the editing complex. Double-stranded RNA interference efficiently depleted band III protein and demonstrated that band III expression is essential for growth of procyclic trypanosomes and for RNA editing. These depleted cell extracts were deficient specifically in guide RNA-directed endonuclease cleavage at both U deletion and U insertion sites and in the activity of the band IV ligase, but they retained the 3′-U-exonuclease and terminal-U-transferase activities as well as band V ligase of the editing complex. Loss of band III protein also resulted in almost complete loss of the band IV ligase protein and altered sedimentation of the band V ligase. These data indicate that band III is either the RNA editing endonuclease or a factor critical for cleavage activity in the editing complex. They also demonstrate that band III is required for proper assembly of the editing complex.

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Wilson, Thomas E., Ulf Grawunder, and Michael R. Lieber. "Yeast DNA ligase IV mediates non-homologous DNA end joining." Nature 388, no. 6641 (July 1997): 495–98. http://dx.doi.org/10.1038/41365.

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33

Hammel, Michal, Yaping Yu, Shujuan Fang, Susan P. Lees-Miller, and John A. Tainer. "XLF Regulates Filament Architecture of the XRCC4·Ligase IV Complex." Structure 18, no. 11 (November 2010): 1431–42. http://dx.doi.org/10.1016/j.str.2010.09.009.

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34

Lee, Y. "Defective neurogenesis resulting from DNA ligase IV deficiency requires Atm." Genes & Development 14, no. 20 (October 15, 2000): 2576–80. http://dx.doi.org/10.1101/gad.837100.

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35

Kondo, Natsuko, Akihisa Takahashi, Eiichiro Mori, Ken Ohnishi, Peter J. McKinnon, Toshisuke Sakaki, Hiroyuki Nakase, and Takeo Ohnishi. "DNA ligase IV as a new molecular target for temozolomide." Biochemical and Biophysical Research Communications 387, no. 4 (October 2009): 656–60. http://dx.doi.org/10.1016/j.bbrc.2009.07.045.

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Grunebaum, Eyal, Andrea Bates, and Chaim M. Roifman. "Omenn syndrome is associated with mutations in DNA ligase IV." Journal of Allergy and Clinical Immunology 122, no. 6 (December 2008): 1219–20. http://dx.doi.org/10.1016/j.jaci.2008.08.031.

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37

Kim, V. H. D., E. Grunebaum, A. Bates, and C. M. Roifman. "Omenn Syndrome is Associated with Mutations in DNA Ligase IV." Journal of Allergy and Clinical Immunology 123, no. 2 (February 2009): S14. http://dx.doi.org/10.1016/j.jaci.2008.12.064.

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Baumann, Peter, and Thomas R. Cech. "Protection of Telomeres by the Ku Protein in Fission Yeast." Molecular Biology of the Cell 11, no. 10 (October 2000): 3265–75. http://dx.doi.org/10.1091/mbc.11.10.3265.

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Schizosaccharomyces pombe cells survive loss of telomeres by a unique pathway of chromosome circularization. Factors potentially involved in this survival mechanism include the heterodimeric Ku protein and ligase IV, both of which are involved in the repair of DNA double-strand breaks in mammalian cells. Furthermore, Ku plays a role in telomere maintenance as well as in DNA double-strand break repair in Saccharomyces cerevisiae. We have identified Ku and ligase IV homologues in S. pombe and analyzed their functions during normal growth and in cells undergoing senescence. In the absence of either a Ku subunit (pku70 +) or ligase IV (lig4 +), nonhomologous DNA end-joining was severely reduced. Lack of functional Ku led to shorter but stable telomeres and caused striking rearrangements of telomere-associated sequences, indicating a function for Ku in inhibiting recombinational activities near chromosome ends. In contrast to S. cerevisiae, concurrent deletion ofpku70 + and the gene for the catalytic subunit of telomerase (trt1 +) was not lethal, allowing for the first time the dissection of the roles of Ku during senescence. Our results support a model in which Ku protects chromosome termini from nucleolytic and recombinational activities but is not involved in the formation of chromosome end fusions during senescence. The conclusion that nonhomologous end-joining is not required for chromosome circularization was further supported by analysis of survivors in strains lacking the genes for bothtrt1 + and lig4 +.

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Palmbos, Phillip L., James M. Daley, and Thomas E. Wilson. "Mutations of the Yku80 C Terminus and Xrs2 FHA Domain Specifically Block Yeast Nonhomologous End Joining." Molecular and Cellular Biology 25, no. 24 (December 15, 2005): 10782–90. http://dx.doi.org/10.1128/mcb.25.24.10782-10790.2005.

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ABSTRACT The nonhomologous end-joining (NHEJ) pathway of DNA double-strand break repair requires three protein complexes in Saccharomyces cerevisiae: MRX (Mre11-Rad50-Xrs2), Ku (Ku70-Ku80), and DNA ligase IV (Dnl4-Lif1-Nej1). Much is known about the interactions that mediate the formation of each complex, but little is known about how they act together during repair. A comprehensive yeast two-hybrid screen of the NHEJ factors of S. cerevisiae revealed all known interactions within the MRX, Ku, and DNA ligase IV complexes, as well as three additional, weaker interactions between Yku80-Dnl4, Xrs2-Lif1, and Mre11-Yku80. Individual and combined deletions of the Yku80 C terminus and the Xrs2 forkhead-associated (FHA) domain were designed based on the latter two-hybrid results. These deletions synergistically blocked NHEJ but not the telomere and recombination functions of Ku and MRX, confirming that these protein regions are functionally important specifically for NHEJ. Further mutational analysis of Yku80 identified a putative C-terminal amphipathic α-helix that is both required for its NHEJ function and strikingly similar to a DNA-dependent protein kinase interaction motif in human Ku80. These results identify a novel role in yeast NHEJ for the poorly characterized Ku80 C-terminal and Xrs2 FHA domains, and they suggest that redundant binding of DNA ligase IV facilitates completion of this DNA repair event.

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Unal, Sule, Karen Cerosaletti, Mustafa Tekin, Mualla Cetin, Duygu Uckan-Cetinkaya, and Fatma Gumruk. "Successful Hematopoietic Stem Cell Transplantation in a Patient with a Novel DNA Ligase IV Mutation." Blood 110, no. 11 (November 16, 2007): 5043. http://dx.doi.org/10.1182/blood.v110.11.5043.5043.

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Abstract DNA Ligase IV deficiency syndrome (LIG4 syndrome) is a rare autosomal recessive disorder caused by mutations in the DNA ligase IV gene (LIG4), which is essential for the repair of DNA double-strand breaks in mamalian cells by non-homologous end joining (O’Driscoll et al, 2001; Critchlow et al, 1998). LIG4-deficient patients are characterized by microcephaly, growth retardation, developmental delay, low birth weight, dysmorphic facial findings called bird-like face, immunodeficiency, pancytopenia, and pronounced clinical and cellular radiosensitivity (O’Driscoll et al, 2001). Herein, we report two siblings with a novel DNA ligase IV mutation, one of whom underwent hematopoietic stem cell transplantation (HSCT). Case 1, was a 10 year-old girl, whose pancytopenia started at 4 years of age. History revealed a birth weight of 2400 g. There was a first-degree consanguinity between parents. Body weight, height, and head circumference were below the third percentile. Low anterior hairline, prominent nasal bridge and bilateral epicanthus were present. Recurrent upper respiratory infection (URI) history was striking. Serum IgM was low for age. Pancytopenia deepened progressively and HSCT was performed from 6/6 HLA matched father after non-myeloablative conditioning; however autologous reconstruction developed and a 2nd HSCT was performed after busulfan, cyclophosphamide and ATG conditioning. Engraftment was achieved by +12 day. Case 2 was a 6 year-old boy, presented with widespread echymoses at three years of age. Microcephaly, body weight and height below the third percentile, inguinal hernia, prominent nasal bridge and bilateral epicanthi were positive findings. History revealed recurrent URI. Serum IgG and IgM were low for age. DEB and mitomycin-C induced chromosomal analyses were within normal limits, whereas spontaneous breakage was found to be increased. Bone marrow examination revealed hypercellularity in both siblings. Alpha-fetoprotein levels were within normal limits. Mutation analysis for Nijmegen breakage syndrome was negative, however sequencing revealed a novel mutation in the LIG4 gene. A homozygous sequence variant, 1762delAAG, which results in the amino acid deletion 588delK, was identified in case 2. Both parents were heterozygous for the alteration. This novel mutation is located in a highly conserved peptide in the ligase IV protein, adjacent to the ligase domain, with previously unknown function (Wei et al, 1995). Our results demonstrate that non-myeloablative conditioning may not be adequate for LIG4 syndrome patients with hypercellular bone marrow. However, successful treatment of LIG4 syndrome can be achieved by HSCT after more potent conditioning.

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Mills, K. D. "Rad54 and DNA Ligase IV cooperate to maintain mammalian chromatid stability." Genes & Development 18, no. 11 (June 1, 2004): 1283–92. http://dx.doi.org/10.1101/gad.1204304.

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42

So, Sairei, Noritaka Adachi, Michael R. Lieber, and Hideki Koyama. "Genetic Interactions between BLM and DNA Ligase IV in Human Cells." Journal of Biological Chemistry 279, no. 53 (October 26, 2004): 55433–42. http://dx.doi.org/10.1074/jbc.m409827200.

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Riballo, Enriqueta, Lisa Woodbine, Thomas Stiff, Sarah A. Walker, Aaron A. Goodarzi, and Penny A. Jeggo. "XLF-Cernunnos promotes DNA ligase IV–XRCC4 re-adenylation following ligation." Nucleic Acids Research 37, no. 2 (December 4, 2008): 482–92. http://dx.doi.org/10.1093/nar/gkn957.

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Dard, Rodolphe, Bérénice Herve, Thierry Leblanc, Jean-Pierre de Villartay, Laura Collopy, Tom Vulliami, Severine Drunat, et al. "DNA ligase IV deficiency: Immunoglobulin class deficiency depends on the genotype." Pediatric Allergy and Immunology 28, no. 3 (February 22, 2017): 298–303. http://dx.doi.org/10.1111/pai.12694.

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Jiao, Keping, Juan Qin, Yumei Zhao, and Honglian Zhang. "Genetic effects of XRCC4 and ligase IV genes on human glioma." NeuroReport 27, no. 14 (September 2016): 1024–30. http://dx.doi.org/10.1097/wnr.0000000000000649.

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46

Kondo, Natsuko, Akihisa Takahashi, Eiichiro Mori, Taichi Noda, Xiaoming Su, Ken Ohnishi, Peter J. McKinnon, et al. "DNA ligase IV is a potential molecular target in ACNU sensitivity." Cancer Science 101, no. 8 (April 10, 2010): 1881–85. http://dx.doi.org/10.1111/j.1349-7006.2010.01591.x.

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Brunet, Barbara A., and Nina Dave. "Unique heterozygous presentation in an infant with DNA ligase IV syndrome." Annals of Allergy, Asthma & Immunology 119, no. 4 (October 2017): 379–80. http://dx.doi.org/10.1016/j.anai.2017.07.017.

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48

Conlin, Michael P., Dylan A. Reid, George W. Small, Howard H. Chang, Go Watanabe, Michael R. Lieber, Dale A. Ramsden, and Eli Rothenberg. "DNA Ligase IV Guides End-Processing Choice during Nonhomologous End Joining." Cell Reports 20, no. 12 (September 2017): 2810–19. http://dx.doi.org/10.1016/j.celrep.2017.08.091.

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49

Murray, Jennie E., Louise S. Bicknell, Gökhan Yigit, Angela L. Duker, Margriet van Kogelenberg, Sara Haghayegh, Dagmar Wieczorek, et al. "Extreme Growth Failure is a Common Presentation of Ligase IV Deficiency." Human Mutation 35, no. 1 (November 8, 2013): 76–85. http://dx.doi.org/10.1002/humu.22461.

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50

Joshi, Rashmi, Surya Jyoti Banerjee, Jennifer Curtiss, and Amanda K. Ashley. "DNA ligase IV mutations confer shorter lifespan and increased sensitivity to nutrient stress in Drosophila melanogaster." Journal of Applied Genetics 63, no. 1 (November 24, 2021): 141–44. http://dx.doi.org/10.1007/s13353-021-00637-0.

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AbstractThe nonhomologous end-joining pathway is a primary DNA double-strand break repair pathway in eukaryotes. DNA ligase IV (Lig4) catalyzes the final step of DNA end ligation in this pathway. Partial loss of Lig4 in mammals causes Lig4 syndrome, while complete loss is embryonically lethal. DNA ligase 4 (DNAlig4) null Drosophila melanogaster is viable, but sensitive to ionizing radiation during early development. We proposed to explore if DNAlig4 loss induced other long-term sensitivities and defects in D. melanogaster. We demonstrated that DNAlig4 mutant strains had decreased lifespan and lower resistance to nutrient deprivation, indicating Lig4 is required for maintaining health and longevity in D. melanogaster.

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