Dna Ligase IEdit
DNA ligase I is a highly conserved nuclear enzyme that seals breaks in the sugar-phosphate backbone of DNA. By forming a phosphodiester bond between adjacent nucleotides, it converts nicks into continuous strands. This ligation step is essential for genome integrity, particularly during the replication of the lagging strand and during several DNA repair pathways. In eukaryotes, the reaction uses Adenosine triphosphate as the energy source, whereas bacterial ligases rely on NAD+-dependent chemistry. In humans, DNA ligase I is encoded by the LIG1 and functions in concert with the replication machinery, including the sliding clamp PCNA, to coordinate nick repair with synthesis on the leading and lagging strands.
The enzyme’s activities are a central part of how cells preserve genome stability. Its primary role is to seal nicks that arise after the removal of RNA primers during DNA replication on the lagging strand, thereby joining the newly synthesized fragments into a continuous strand. Beyond replication, DNA ligase I participates in repair processes such as base excision repair and nucleotide excision repair by sealing gaps created during repair synthesis. Its action complements other ligases, including DNA ligase III and DNA ligase IV, in a network that preserves genome integrity across cellular states and tissues.
Function
- Lagging-strand synthesis: after RNA primers are removed and DNA is filled in, DNA ligase I closes nicks between adjacent Okazaki fragments to establish a continuous strand of DNA replication.
- DNA repair: during BER and NER, ligase I seals the final nick once repair synthesis has filled in the damaged region.
- Coordination with replication factors: the enzyme is recruited to replication sites by interactions with PCNA and other components of the replication complex, ensuring timely ligation as synthesis proceeds.
- Substrate specificity: while it acts primarily on nicked duplex DNA, ligase I can seal a variety of 5'-phosphate and 3'-OH termini generated during repair and replication.
Mechanistically, DNA ligase I operates via a three-step catalytic cycle. First, the enzyme becomes adenylated by ATP, forming an enzyme–adenylate intermediate. Next, the adenylyl group is transferred to the 5' phosphate at the nick, producing a DNA–adenylate intermediate while freeing a 3'-OH to be joined. Finally, the 3'-OH attacks the activated 5'–P, displacing AMP and creating the intact phosphodiester linkage. This cycle is tightly integrated with the cell's replication fork, where the synthesis machinery leaves behind nicks that ligase I promptly seals.
Structure and domains
DNA ligase I is organized to engage both DNA substrates and partner proteins. Its N-terminal region contains motifs that mediate interaction with PCNA through a PIP-box, helping tether the enzyme to sites of replication. The central region houses the catalytic core responsible for adenylylation and phosphodiester bond formation, while a C-terminal region supports DNA binding and, in some species, additional protein–protein interactions. In many eukaryotes, features such as BRCT-like domains or adjacent interaction surfaces facilitate coordination with other repair factors, polymerases, and processing enzymes.
Regulation of DNA ligase I expression and activity is linked to the cell cycle. Expression tends to rise during S-phase, aligning ligation capacity with the surge in replication-dependent nick formation. Post-translational modifications and interactions with replication factors modulate catalytic efficiency and substrate access, ensuring ligation does not lag behind synthesis or repair demands.
In humans and other organisms
Most eukaryotes rely on a DNA ligase I–type enzyme for the synthesis-associated ligation step, whereas bacterial and some archaeal systems use distinct ligases with different cofactor requirements. The human enzyme is a product of the LIG1 and participates in widespread genome maintenance tasks beyond a single pathway. In model organisms, loss or reduction of ligase I activity can slow replication, increase sensitivity to DNA-damaging agents, and perturb development.
Mutations in LIG1 have been described in humans, giving rise to a syndrome characterized by immunodeficiency, microcephaly, growth retardation, and developmental abnormalities. The phenotype underscores ligase I’s importance for proliferating tissues and for maintaining genomic stability during rapid cell division. In oncology, altered expression of ligase I has been observed in certain cancers, and researchers explore its potential as a biomarker or as a therapeutic target in contexts of replication stress and DNA repair deficiency.
Controversies and debates around DNA ligase I tend to center on its essentiality versus redundancy and the therapeutic potential of targeting the enzyme. While ligase I is crucial for replication and repair, cells also harbor complementary ligases (notably DNA ligase III and DNA ligase IV) that can partially compensate under some conditions. This redundancy complicates the development of highly selective inhibitors that kill cancer cells without intolerable effects on normal tissue. Proposals to exploit ligase I inhibition in cancer therapy emphasize combination strategies that sensitize tumor cells to DNA-damaging agents or synthetic lethal interactions with other repair defects, while aiming to minimize harm to normal cells.
A related discussion concerns the differentiation of ligase I function from the broader ligase family in evolutionary terms. The ATP-dependent ligases of eukaryotes have diverged from NAD+-dependent bacterial ligases, reflecting distinct regulatory contexts and substrate processing needs in different kingdoms. Understanding these differences informs both basic biology and the development of selective inhibitors that could, in theory, treat diseases associated with replication stress or repair deficiency.