DNA ligase I variants fail in the ligation of mutagenic repair intermediates with mismatches and oxidative DNA damage

Abstract DNA ligase I (LIG1) joins DNA strand breaks during DNA replication and repair transactions and contributes to genome integrity. The mutations (P529L, E566K, R641L and R771W) in LIG1 gene are described in patients with LIG1-deficiency syndrome that exhibit immunodeficiency. LIG1 senses 3’-DNA ends with a mismatch or oxidative DNA base inserted by a repair DNA polymerase. However, the ligation efficiency of the LIG1 variants for DNA polymerase-promoted mutagenesis products with 3’-DNA mismatches or 8-oxo-2’-deoxyguanosine (8-oxodG) remains undefined. Here, we report that R641L and R771W fail in the ligation of nicked DNA with 3’-8-oxodG, leading to an accumulation of 5’-AMP-DNA intermediates in vitro. Moreover, we found that the presence of all possible 12 non-canonical base pairs variously impacts the ligation efficiency by P529L and R771W depending on the architecture at the DNA end, whereas E566K exhibits no activity against all substrates tested. Our results contribute to the understanding of the substrate specificity and mismatch discrimination of LIG1 for mutagenic repair intermediates and the effect of non-synonymous mutations on ligase fidelity.

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The human checkpoint sensor and alternative DNA clamp Rad9–Rad1–Hus1 modulates the activity of DNA ligase I, a component of the long-patch base excision repair machinery

Biochemical Journal ◽

10.1042/bj20050211 ◽

2005 ◽

Vol 389 (1) ◽

pp. 13-17 ◽

Cited By ~ 41

Author(s):

Ekaterina SMIRNOVA ◽

Magali TOUEILLE ◽

Enni MARKKANEN ◽

Ulrich HÜBSCHER

Keyword(s):

Quality Control ◽

Dna Polymerase ◽

Base Excision Repair ◽

Excision Repair ◽

Dna Ligase ◽

Dna Polymerase Β ◽

Flap Endonuclease 1 ◽

Important Target ◽

Dna Ligase I ◽

Base Excision

The human checkpoint sensor and alternative clamp Rad9–Rad1–Hus1 can interact with and specifically stimulate DNA ligase I. The very recently described interactions of Rad9–Rad1–Hus1 with MutY DNA glycosylase, DNA polymerase β and Flap endonuclease 1 now complete our view that the long-patch base excision machinery is an important target of the Rad9–Rad1–Hus1 complex, thus enhancing the quality control of DNA.

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Thermodynamics of Human DNA Ligase I Trimerization and Association with DNA Polymerase β

Journal of Biological Chemistry ◽

10.1074/jbc.273.32.20540 ◽

1998 ◽

Vol 273 (32) ◽

pp. 20540-20550 ◽

Cited By ~ 48

Author(s):

Emilios K. Dimitriadis ◽

Rajendra Prasad ◽

Mary K. Vaske ◽

Ling Chen ◽

Alan E. Tomkinson ◽

...

Keyword(s):

Dna Polymerase ◽

Dna Ligase ◽

Dna Polymerase Β ◽

Human Dna ◽

Dna Ligase I

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The ligation of pol β mismatch insertion products governs the formation of promutagenic base excision DNA repair intermediates

Nucleic Acids Research ◽

10.1093/nar/gkaa151 ◽

2020 ◽

Vol 48 (7) ◽

pp. 3708-3721 ◽

Cited By ~ 4

Author(s):

Melike Çağlayan

Keyword(s):

Excision Repair ◽

Dna Ligase ◽

Active Site Residues ◽

Dna Ligases ◽

Terminal Domain ◽

Dna Ligase I ◽

Nucleotide Insertion ◽

Base Excision ◽

Ligation Step

Abstract DNA ligase I and DNA ligase III/XRCC1 complex catalyze the ultimate ligation step following DNA polymerase (pol) β nucleotide insertion during base excision repair (BER). Pol β Asn279 and Arg283 are the critical active site residues for the differentiation of an incoming nucleotide and a template base and the N-terminal domain of DNA ligase I mediates its interaction with pol β. Here, we show inefficient ligation of pol β insertion products with mismatched or damaged nucleotides, with the exception of a Watson–Crick-like dGTP insertion opposite T, using BER DNA ligases in vitro. Moreover, pol β N279A and R283A mutants deter the ligation of the promutagenic repair intermediates and the presence of N-terminal domain of DNA ligase I in a coupled reaction governs the channeling of the pol β insertion products. Our results demonstrate that the BER DNA ligases are compromised by subtle changes in all 12 possible noncanonical base pairs at the 3′-end of the nicked repair intermediate. These findings contribute to understanding of how the identity of the mismatch affects the substrate channeling of the repair pathway and the mechanism underlying the coordination between pol β and DNA ligase at the final ligation step to maintain the BER efficiency.

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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 ◽

10.1128/mcb.15.6.3206 ◽

1995 ◽

Vol 15 (6) ◽

pp. 3206-3216 ◽

Cited By ~ 164

Author(s):

Y F Wei ◽

P Robins ◽

K Carter ◽

K Caldecott ◽

D J Pappin ◽

...

Keyword(s):

Dna Repair ◽

Cdna Clone ◽

Dna Ligase ◽

Dna Ligases ◽

Dna Ligase Iv ◽

Ligase Iv ◽

Dna Ligase I ◽

Cloned Cdna ◽

Dna Ligase Iii

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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A novel interaction between DNA ligase III and DNA polymerase γ plays an essential role in mitochondrial DNA stability

Biochemical Journal ◽

10.1042/bj20061004 ◽

2007 ◽

Vol 402 (1) ◽

pp. 175-186 ◽

Cited By ~ 14

Author(s):

Ananya De ◽

Colin Campbell

Keyword(s):

Mitochondrial Dna ◽

Dna Polymerase ◽

Mitochondrial Protein ◽

Dna Ligase ◽

Zinc Finger Domain ◽

Wild Type ◽

Mitochondrial Dna Copy Number ◽

Dna Polymerase Γ ◽

Dna Ligase Iii

The data in the present study show that DNA polymerase γ and DNA ligase III interact in mitochondrial protein extracts from cultured HT1080 cells. An interaction was also observed between the two recombinant proteins in vitro. Expression of catalytically inert versions of DNA ligase III that bind DNA polymerase γ was associated with reduced mitochondrial DNA copy number and integrity. In contrast, overexpression of wild-type DNA ligase III had no effect on mitochondrial DNA copy number or integrity. Experiments revealed that wild-type DNA ligase III facilitates the interaction of DNA polymerase γ with a nicked DNA substrate in vitro, and that the zinc finger domain of DNA ligase III is required for this activity. Mitochondrial protein extracts prepared from cells overexpressing a DNA ligase III protein that lacked the zinc finger domain had reduced base excision repair activity compared with extracts from cells overexpressing the wild-type protein. These data support the interpretation that the interaction of DNA ligase III and DNA polymerase γ is required for proper maintenance of the mammalian mitochondrial genome.

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Distinct pools of proliferating cell nuclear antigen associated to DNA replication sites interact with the p125 subunit of DNA polymerase δ or DNA ligase I

Experimental Cell Research ◽

10.1016/j.yexcr.2003.10.025 ◽

2004 ◽

Vol 293 (2) ◽

pp. 357-367 ◽

Cited By ~ 21

Author(s):

Federica Riva ◽

Monica Savio ◽

Ornella Cazzalini ◽

Lucia A Stivala ◽

Ivana A Scovassi ◽

...

Keyword(s):

Dna Replication ◽

Dna Polymerase ◽

Proliferating Cell Nuclear Antigen ◽

Nuclear Antigen ◽

Dna Ligase ◽

Dna Polymerase Δ ◽

Dna Ligase I ◽

Replication Sites ◽

Proliferating Cell

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Cylindrospermopsin-Microcystin-LR Combinations May Induce Genotoxic and Histopathological Damage in Rats

Toxins ◽

10.3390/toxins12060348 ◽

2020 ◽

Vol 12 (6) ◽

pp. 348 ◽

Cited By ~ 2

Author(s):

Leticia Díez-Quijada ◽

Concepción Medrano-Padial ◽

María Llana-Ruiz-Cabello ◽

Giorgiana M. Cătunescu ◽

Rosario Moyano ◽

...

Keyword(s):

Bone Marrow ◽

Dna Damage ◽

Oxidative Dna Damage ◽

Fatty Degeneration ◽

Dna Strand Breaks ◽

Histopathological Study ◽

Strand Breaks ◽

Dna Strand

Cylindrospermopsin (CYN) and microcystins (MC) are cyanotoxins that can occur simultaneously in contaminated water and food. CYN/MC-LR mixtures previously investigated in vitro showed an induction of micronucleus (MN) formation only in the presence of the metabolic fraction S9. When this is the case, the European Food Safety Authority recommends a follow up to in vivo testing. Thus, rats were orally exposed to 7.5 + 75, 23.7 + 237, and 75 + 750 μg CYN/MC-LR/kg body weight (b.w.). The MN test in bone marrow was performed, and the standard and modified comet assays were carried out to measure DNA strand breaks or oxidative DNA damage in stomach, liver, and blood cells. The results revealed an increase in MN formation in bone marrow, at all the assayed doses. However, no DNA strand breaks nor oxidative DNA damage were induced, as shown in the comet assays. The histopathological study indicated alterations only in the highest dose group. Liver was the target organ showing fatty degeneration and necrotic hepatocytes in centrilobular areas, as well as a light mononuclear inflammatory periportal infiltrate. Additionally, the stomach had flaking epithelium and mild necrosis of epithelial cells. Therefore, the combined exposure to cyanotoxins may induce genotoxic and histopathological damage in vivo.

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Phosphorylation of Serine 51 Regulates the Interaction of Human DNA Ligase I with Replication Factor C and Its Participation in DNA Replication and Repair

Journal of Biological Chemistry ◽

10.1074/jbc.m112.383570 ◽

2012 ◽

Vol 287 (44) ◽

pp. 36711-36719 ◽

Cited By ~ 11

Author(s):

Zhimin Peng ◽

Zhongping Liao ◽

Barbara Dziegielewska ◽

Yoshi Matsumoto ◽

Stefani Thomas ◽

...

Keyword(s):

Dna Replication ◽

Dna Ligase ◽

Replication Factor C ◽

Replication Factor ◽

Human Dna ◽

Dna Ligase I ◽

Dna Replication And Repair ◽

Factor C

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Identification of a novel human DNA ligase I inhibitor that promotes cellular apoptosis in DLD-1 cells: an in silico and in vitro mechanistic study

RSC Advances ◽

10.1039/c6ra22364h ◽

2016 ◽

Vol 6 (97) ◽

pp. 94574-94587 ◽

Cited By ~ 3

Author(s):

Deependra Kumar Singh ◽

Mohd. Kamil Hussain ◽

Shagun Krishna ◽

Amit Laxmikant Deshmukh ◽

Mohammad Shameem ◽

...

Keyword(s):

In Silico ◽

Specific Inhibitor ◽

Mechanistic Study ◽

Dna Ligase ◽

Dna Ligases ◽

Human Dna ◽

Dna Ligase I ◽

Cellular Apoptosis

The compound S-097/98 is a specific inhibitor of hLig1. As shown in the figure, the compound inhibits only hLig1 while other human and non-human DNA ligases are not inhibited.

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