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.

DNA ligase I fidelity mediates the mutagenic ligation of pol β oxidized and mismatch nucleotide insertion products in base excision repair

“…We previously demonstrated that the nicked repair product of pol β 8-oxodGTP insertion cannot be used as a DNA substrate by LIG1 during substrate-product channeling at the downstream steps of BER (12)(13)(14)(15)(16). In the present study, we first evaluated the effect of low-fidelity LIG1 for the ligation of pol β 8-oxodGTP insertion products in vitro.…”

“…Human DNA polymerases and LIGs have been considered as key determinants of genome integrity (11). In our previous studies, we demonstrated the importance of the coordination between DNA polymerase (pol) β and LIG1 during the repair of single DNA base lesions through base excision repair (BER) (9,10,(12)(13)(14)(15)(16). BER is a critical process for preventing the mutagenic and lethal consequences of DNA damage that arises from endogenous and environmental agents and underlies disease and aging (17,18).…”

“…For example, pol β performs mutagenic repair by inserting 8-oxodGTP opposite adenine within an active site that exhibits a frayed structure because of the lack of base pairing with a template base after the oxidized nucleotide insertion (25). In our prior studies, we demonstrated that pol β 8-oxodGTP insertion confounds the DNA ligation step of the BER pathway and leads to the formation of a ligation failure product with a 5'-adenylate (AMP) block (12)(13)(14). We also reported the effect of pol β mismatch nucleotide insertion on the substrate-product channeling to LIG1 during the final steps of BER and the fidelity of this mechanism in the presence of the epigenetically important 5-methylcytosine base modifications (15,16).…”

DNA ligase I fidelity mediates the mutagenic ligation of pol β oxidized nucleotide insertion products and base excision repair intermediates with mismatches

“…For example, the reiteration of the mutations identified in the LIG1 gene of human patients who exhibit the symptoms of developmental abnormalities, immunodeficiency and lymphoma, in a mouse model has proven that LIG1 deficiency causes genetic instability and predisposition to cancer (49–53). Recently, we reported that the LIG1 variants associated with LIG1-deficiency disease exhibits different ligation fidelity for DNA polymerase-promoted mutagenesis products (14). Moreover, the studies have been suggested a pivotal role for pol β-mediated high-fidelity nucleotide insertion during gap filling step of BER pathway in the prevention of carcinogenesis (54).…”

“…For example, pol β performs mutagenic repair by inserting 8-oxodGTP opposite Adenine at the active site that exhibits a frayed structure with lack of base pairing with a template base after the insertion (25). In our prior studies, we demonstrated that pol β 8-oxodGTP insertion confounds the DNA ligation step of BER pathway and leads to the formation of ligation failure product with 5’-adenylate (AMP) block (12–14). We also reported the effect of pol β mismatch nucleotide insertion on the substrate-product channeling to LIG1 during the final steps of BER and the fidelity of this mechanism in the presence of epigenetically important 5-methylcytosine base modifications (15, 16).…”