DNA ligases catalyse the joining of single and double‐strand DNA breaks, which is an essential final step in DNA replication, recombination and repair. Mammalian cells have four DNA ligases, termed ligases I–IV. In contrast, other than a DNA ligase I homologue (encoded by CDC9), no other DNA ligases have hitherto been identified in Saccharomyces cerevisiae. Here, we report the identification and characterization of a novel gene, LIG4, which encodes a protein with strong homology to mammalian DNA ligase IV. Unlike CDC9, LIG4 is not essential for DNA replication, RAD52‐dependent homologous recombination nor the repair of UV light‐induced DNA damage. Instead, it encodes a crucial component of the non‐homologous end‐joining (NHEJ) apparatus, which repairs DNA double‐strand breaks that are generated by ionizing radiation or restriction enzyme digestion: a function which cannot be complemented by CDC9. Lig4p acts in the same DNA repair pathway as the DNA end‐binding protein Ku. However, unlike Ku, it does not function in telomere length homeostasis. These findings indicate diversification of function between different eukaryotic DNA ligases. Furthermore, they provide insights into mechanisms of DNA repair and suggest that the NHEJ pathway is highly conserved throughout the eukaryotic kingdom.

In response to DNA damage, cells engage a complex set of events that together comprise the DNA-damage response (DDR). These events bring about the repair of the damage and also slow down or halt cell cycle progression until the damage has been removed. In stark contrast, the ends of linear chromosomes, telomeres, are generally not perceived as DNA damage by the cell even though they terminate the DNA double-helix. Nevertheless, it has become clear over the past few years that many proteins involved in the DDR, particularly those involved in responding to DNA double-strand breaks, also play key roles in telomere maintenance. In this review, we discuss the current knowledge of both the telomere and the DDR, and then propose an integrated model for the events associated with the metabolism of DNA ends in these two distinct physiological contexts.All organisms respond to interruptions in the DNA double-helix by promptly launching the DNA-damage response (DDR). This involves the mobilization of DNArepair factors and the activation of pathways, often termed checkpoint pathways, which temporarily or permanently delay cell cycle progression. Although the integrity of the DNA double-helix is perturbed by telomeres (the ends of linear chromosomes), these structures generally escape activating the DDR. Several explanations have been proposed to explain the exceptional nature of telomeres in this regard. Thus, it has been suggested that a telomere might not be recognized by components of the DDR because of its unique DNA sequence and structure, its specific localization within the cell nucleus, and/or because of the actions of specific proteins associated with it. Although this is partly correct, recent findings have revealed that, contrary to initial expectations, various proteins involved in the DDR physically associate with telomeres and actually play important roles in regulating normal telomeric functions. In this review, we focus on the role of DDR factors in regulating telomere length and stability, and also explain how dysfunctional telomeres can trigger the DDR. Before doing this, however, we first summarize the salient features of both telomeres and the DDR. Telomere structure and biologyThe ends of linear chromosomes contain long stretches of DNA tandem repeats (TTAGGG in vertebrates) and terminate in a 3Ј protruding single-stranded DNA overhang. Due to the inability of the standard lagging-strand DNA replication machinery to copy the most distal telomere sequences (i.e., those at the very end of the chromosome) and to the additional exonucleolytic processing needed to generate protruding overhangs at both ends, telomeric DNA progressively decreases in length as cells go through successive division cycles. Hence, in the absence of specialized telomere homeostatic mechanisms this would ultimately lead to the loss of all telomeric sequences and subsequently to the loss of more internal essential genetic information and ensuing cell death. To circumvent this, many cells maintain their telomeres by the action of telo...

High-mobility-group protein 1 (HMG1) is an abundant, non-sequence-specific, chromosomal protein with two homologous, HMG-box, DNA-binding domains, A and B, and an acidic tail. The HMG-box motif also occurs, as a single copy, in some sequence-specific transcription factors, e.g. the sex-determining factor, SRY. We have investigated whether or not there are differences in the DNA-binding properties of the isolated A and B HMG-box domains of HMG1 and SRY and whether, in the case of A and B, there might also be differences due to different sequence contexts within the native protein. The basic regions that flank the HMG1 B box, giving B', enhance its DNA-binding, supercoiling and DNA-bending activities, and promote the self-association of the DNA-bound B-box. All the HMG-box domains bind with structure specificity to four-way junctions, but the structure selectivity is significantly greater for A and the SRY box than for the HMG1 B or B' domains, as judged by competition with excess plasmid DNA. The domains self-associate to different extents on supercoiled DNA and this may explain differences in the ability to discriminate between four-way junctions and supercoiled DNA. The HMG1 A, B and B' domains constrain negative superhelical turns in DNA, but the SRY HMG box does not. Only the full B domain (B') bends DNA in a ligase-mediated circularisation assay; the minimal B box, the A domain and the SRY box do not. Thus, despite a common global fold, the HMG box appears to have been adapted to various functions in different protein contexts.

High-mobility-group protein 1 (HMG1) is a conserved chromosomal protein with two homologous DNA-binding HMG-box domains, A and B, linked by a short basic region to an acidic carboxy-terminal tail. NMR spectroscopy on the free didomain (AB) shows that the two HMG boxes do not interact. The didomain has a higher affinity for all DNA substrates tested than single HMG-box domains and has a significantly higher ability to distort DNA by bending and supercoiling. The interaction of the didomain with DNA is stabilized by the presence of the basic region (Ϸ20 residues, 9 of which are Lys) that links the second HMG box to the acidic tail in intact HMG1; this may be, at least in part, why this region also enhances supercoiling of relaxed circular DNA by the didomain and circularization of short DNA fragments (in the presence of ligase). Competition assays suggest significantly different structure-specific preferences of single and tandem HMG boxes for four-way junction and supercoiled plasmid DNA. Binding to supercoiled DNA appears to be promoted by protein oligomerization, which is pronounced for the didomains. Electron microscopy suggests that the oligomers are globular aggregates, associated with DNA looping. One box versus two (or several) is likely to be an important determinant of the properties of (non-sequence specific) HMG-box proteins.Keywords : high-mobility-group protein 1 (HMG1) ; four-way junction ; DNA bending; supercoiling ; NMR.High-mobility-group proteins 1 and 2 (HMG1 and 2) are cave face of the protein domain [18, 22]