Crucial role for DNA ligase III in mitochondria but not in Xrcc1-dependent repair

Abstract

Mammalian cells contain three different DNA ligase enzymes, each with different properties but all involved in DNA replication and repair. Ligase III (Lig3) is known to form a complex with the nuclear DNA repair protein Xrcc1, and Lig3 null animals cannot be made. This raises the question of whether this nuclear role in base-excision repair (BER) is the critical function of Lig3 that maintains viability. Two groups reporting in this issue of Nature investigate different aspects of Lig3 function in vivo, both concluding that the catalytic activity of Lig3 is critical for mitochondrial DNA maintenance and viability, but unexpectedly, is dispensable for Xrcc1-mediated nuclear BER. These findings suggest that Lig3 mutations might cause some of the human syndromes associated with defects in the replication and/or repair of mitochondrial DNA. Eukaryotic cells have several DNA ligases. DNA ligase III (Lig3) forms a complex with Xrcc1 that can function in nuclear repair. But, Lig3 null animals cannot be made; is this nuclear role in base excision repair its critical function? This is one of two papers showing that the role of Lig3 in the nucleus is non-essential. Rather, the catalytic activity of Lig3, but not Xrcc1, is essential for the maintenance of mitochondria. Mammalian cells have three ATP-dependent DNA ligases, which are required for DNA replication and repair1. Homologues of ligase I (Lig1) and ligase IV (Lig4) are ubiquitous in Eukarya, whereas ligase III (Lig3), which has nuclear and mitochondrial forms, appears to be restricted to vertebrates. Lig3 is implicated in various DNA repair pathways with its partner protein Xrcc1 (ref. 1). Deletion of Lig3 results in early embryonic lethality in mice, as well as apparent cellular lethality2, which has precluded definitive characterization of Lig3 function. Here we used pre-emptive complementation to determine the viability requirement for Lig3 in mammalian cells and its requirement in DNA repair. Various forms of Lig3 were introduced stably into mouse embryonic stem (mES) cells containing a conditional allele of Lig3 that could be deleted with Cre recombinase. With this approach, we find that the mitochondrial, but not nuclear, Lig3 is required for cellular viability. Although the catalytic function of Lig3 is required, the zinc finger (ZnF) and BRCA1 carboxy (C)-terminal-related (BRCT) domains of Lig3 are not. Remarkably, the viability requirement for Lig3 can be circumvented by targeting Lig1 to the mitochondria or expressing Chlorella virus DNA ligase, the minimal eukaryal nick-sealing enzyme3, or Escherichia coli LigA, an NAD+-dependent ligase1. Lig3-null cells are not sensitive to several DNA-damaging agents that sensitize Xrcc1-deficient cells4,5,6. Our results establish a role for Lig3 in mitochondria, but distinguish it from its interacting protein Xrcc1.