Quality control of DNA break metabolism: in the 'end', it's a good thing

Abstract

DNA ends pose specific problems in the control of genetic information quality. Ends of broken DNA need to be rejoined to avoid genome rearrangements, whereas natural DNA ends of linear chromosomes, telomeres, need to be stable and hidden from the DNA damage response. Efficient DNA end metabolism, either at induced DNA breaks or telomeres, does not result from the machine-like precision of molecular reactions, but rather from messier, more stochastic processes. The necessary molecular interactions are dynamically unstable, with constructive and destructive processes occurring in competition. In the end, quality control comes from the constant building up and tearing down of inappropriate, but also appropriate reaction steps in combination with factors that only slightly shift the equilibrium to eventually favour appropriate events. Thus, paradoxically, enzymes antagonizing DNA end metabolism help to ensure that genome maintenance becomes a robust process.

Figure 1

Metabolism at DNA ends. A schematic representation of DNA end metabolism by homologous recombination (left-hand side, under A), and non-homologous DNA end joining (middle, under B), telomerization (upper right-hand side, under C, and bottom right-hand side, under D). (A) Homologous recombination acts on one-ended DNA breaks that can arise from replication of a damaged template. Recognition and resection of the end yields single-stranded DNA with a 3′ end. Subsequently, a joint molecule is formed by D-loop formation with the identical sequence on the sister chromatid in a reaction mediated by the RAD51 nucleoprotein filament formed on the single-stranded DNA. This reaction involves numerous mediators and/or regulators, including BRCA2 in mammals and Rad52 in S. cerevisiae. The Rad51 nucleoprotein filaments in S. cerevisiae, or RecA nucleoprotein filaments in the bacterium E. coli, that form at inappropriate places and be removed by DNA helicases such as Srs2 and UvrD, respectively. Promiscuous recombination due to the formation of D-loops at incorrect locations can be avoided due to DNA helicases, such as S. cerevisiae Sgs1. Eventually, resolution of the joint between the sister chromatids results in the re-establishment of the replication fork and concludes the accurate repair of the replication-associated one-ended DNA break. (B) Two-ended DNA breaks, resulting from the direct action of DNA-damaging agents on both strands of the DNA, can be acted upon by the non-homologous DNA end-joining core components Ku70/80, DNA–Pkcs, DNA ligase IV, XRCC4, and XLF. When DNA end processing is required to create ligatable ends, endonucleases, such as Artemis, and DNA polymerases can act due to their interaction with the core components located at the ends. Rejoining of DNA breaks need not be accurate at the sequence level, but will avoid deleterious chromosomal translocations. (C) Telomeres, the natural DNA ends of linear chromosomes, are maintained during DNA replication by telomerase. They are protected form the DNA-damage response by their inclusion in a protein complex, termed shelterin. The 3′ single-strand overhang of the telomeric DNA is invaded in upstream telomeric sequences forming a D-loop-like structure, called a T-loop. (D) Conversely, DSBs need to be protected from telomerase action to prevent the formation of telomeres at inappropriate locations. In S. cerevisiae cells, the action of telomerase is antagonized by the Pif1 helicase. After Pif1's action, more appropriate DSB repair processes have another chance to act and seal the break.