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Review
. 2019 May 17;431(11):2068-2081.
doi: 10.1016/j.jmb.2019.04.028. Epub 2019 Apr 26.

Interplay Between DNA Polymerases and DNA Ligases: Influence on Substrate Channeling and the Fidelity of DNA Ligation

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Free PMC article
Review

Interplay Between DNA Polymerases and DNA Ligases: Influence on Substrate Channeling and the Fidelity of DNA Ligation

Melike Çağlayan. J Mol Biol. .
Free PMC article

Abstract

DNA ligases are a highly conserved group of nucleic acid enzymes that play an essential role in DNA repair, replication, and recombination. This review focuses on functional interaction between DNA polymerases and DNA ligases in the repair of single- and double-strand DNA breaks, and discusses the notion that the substrate channeling during DNA polymerase-mediated nucleotide insertion coupled to DNA ligation could be a mechanism to minimize the release of potentially mutagenic repair intermediates. Evidence suggesting that DNA ligases are essential for cell viability includes the fact that defects or insufficiency in DNA ligase are casually linked to genome instability. In the future, it may be possible to develop small molecule inhibitors of mammalian DNA ligases and/or their functional protein partners that potentiate the effects of chemotherapeutic compounds and improve cancer treatment outcomes.

Keywords: DNA ligase; DNA polymerase; DNA repair; genome stability; ligation failure.

Figures

Figure 1.
Figure 1.. Structural domain organization of nuclear human DNA ligases.
DNA ligases contain the N-terminal DNA binding domain (DBD, green) and the C-terminal catalytic core consisting of the adenylation domain (AdD, blue) and the oligonucleotide binding domain (OBD, purple). DNA ligase III isoforms a and β include an N-terminal zinc finger (ZnF, pink). DNA ligases IIIα and IV have a breast and ovarian cancer susceptibility protein-1 C-terminal domain (BRCT, red). While DNA ligases I and IIIβ have a nuclear localization signal (NLS, gray), the N-terminal region of DNA ligase I also contains a replication factory targeting sequence (RFTS, orange) also known as a PCNA-interacting peptide (PIP) box. The active site lysine residues that become adenylated during the first step of ligation reaction in the AdD domain that contains an AMP binding pocket are shown as asterisks.
Figure 2.
Figure 2.. Three chemical sequential steps of DNA ligation reaction.
In the first step, the active site lysine residue in the adenylation domain (AdD, blue) of the DNA ligase interacts with adenosine triphosphate (ATP) and the enzyme becomes adenylated. In the second step, the adenylated ligase binds to and encircles the nicked DNA through the DNA binding (DBD, green) and the oligonucleotide binding (OBD, purple) domains. During this step, the adenosine monophosphate (AMP) is then transferred to the 5′-P end of the nicked DNA. In the third step, the non-adenylated DNA ligase utilizes the 3′-hydroxyl (3′-OH) terminus of the nick as a nucleophile to attack the 5′-adenylated DNA. This results in formation of the phosphodiester bond coupled to release of AMP.
Figure 3.
Figure 3.. Substrate channeling of DNA repair intermediates during single-strand break repair.
The scheme represents base excision repair (BER) pathway that involves several sequential enzymatic steps and hand off between BER proteins during short-patch BER (SP-BER) and long-patch BER (LP-BER) subpathways. A single DNA base damage (i.e., 8-oxoG) is initially removed by a DNA glycosylase, leaving an abasic site that is then processed by AP endonuclease 1 (APE1), leaving 3′-OH and 5′-deoxyribose phosphate (dRP) groups. In the SP-BER subpathway, DNA polymerase (pol) β removes the 5′-dRP group and fills the gap by inserting a single nucleotide (i.e., dGTP). In the LP-BER subpathway, if the dRP group is modified, proliferating cell nuclear antigen (PCNA)-dependent DNA synthesis of 2–13 nucleotides by pol δ/ε or pol β and their removal by Flap Endonuclease 1 (FEN1) occur. DNA ligase IIIα/XRCC1 complex and DNA ligase I joins 3′-OH and 5′-P DNA termini to complete the SP-BER and LP-BER subpathways, respectively.
Figure 4.
Figure 4.. Functional interaction between DNA polymerase β and DNA ligases during base excision repair.
The scheme represents the two possible enzymatic steps in which abortive DNA repair intermediates can be formed as a result of the lack of substrate channeling from DNA polymerase (pol) β to DNA ligase I or DNA ligase IIIα/XRCC1 complex. DNA ligase reaction may abort, and the BER intermediate could become 5′-adenylated, yielding the abortive DNA intermediate with the 5′-AMP-dRP group. Alternatively, pol β oxidized nucleotide (i.e., 8-oxodGTP) insertion opposite the template base A or C may lead to DNA ligase failure and formation of an abortive ligation product with a 3′-inserted oxidized base and a 5′-adenylate group (5′-AMP) on the repair intermediate.
Figure 5.
Figure 5.. Substrate channeling of DNA repair intermediates and functional interaction between DNA polymerase μ and DNA ligase IV during double-strand break repair.
The scheme represents the recruitment of multi-protein complex and hand off between DSB repair proteins during non-homologous end-joining pathway. DNA polymerase μ-mediated dG:T mismatch (dGTP or 8-oxodGTP insertion opposite template base T) insertion may lead to efficient DNA ligation and formation of promutagenic DNA repair intermediate.
Figure 6.
Figure 6.. Protein partners of nuclear human DNA ligases.
(a) The N-terminal domain of DNA ligase I, including the first 232 amino acid residues of the protein, interacts with the N-terminal part of DNA polymerase β harboring an 8 kDa lyase domain that is responsible for 5′-dRP removal. The PIP box of DNA ligase I mediates its interaction with proliferating cell nuclear antigen (PCNA). (b) The ovarian cancer susceptibility protein 1 (BRCT) and zincbinding (ZnF) domains of DNA ligase IIIα mediates protein-protein interactions with X-ray repair cross-complementing protein 1 (XRCC1) and Poly(ADP-Ribose) Polymerase 1 (PARP1), respectively. (c) DNA ligase IV forms a functional complex with X-ray repair crosscomplementing protein 4 (XRCC4) through its two BRCA1 C-terminal (BRCT) domains.

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