The ubiquitous role of ubiquitin in the DNA damage response

Abstract

Protein ubiquitylation has emerged as an important regulatory mechanism that impacts almost every aspect of the DNA damage response. In this review, we discuss how DNA repair and checkpoint pathways utilize the diversity offered by the ubiquitin conjugation system to modulate the response to genotoxic lesions in space and time. In particular, we will highlight recent work done on the regulation of DNA double-strand breaks signalling and repair by the RNF8/RNF168 E3 ubiquitin ligases, the Fanconi anemia pathway and the role of protein degradation in the enforcement and termination of checkpoint signalling. We also discuss the various functions of deubiquitylating enzymes in these processes along with potential avenues for exploiting the ubiquitin conjugation/deconjugation system for therapeutic purposes.

Fig. 1

Ubiquitylation cascade and ubiquitin molecule. (A and B) Schematic representation of the ubiquitylation cascade as it is mediated by the E1, E2 and E3 enzymes and the different types of ubiquitylation (refer to text for details). (C) A high-resolution structure of the ubiquitin molecule (pdb 1ubq). The surface portion containing the indicated lysine residue is shaded red. The two ubiquitin molecules shown are rotated 180° along their y-axis relative to each other.

Fig. 2

Model of RNF8/RNF168-mediated regulatory ubiquitylation at DSBs. (a) DNA damage induces the rapid phosphorylation of histone H2AX, which is recognized by the scaffolding protein MDC1. MDC1 itself is also phosphorylated and directly recruits the E3 ubiquitin ligase RNF8 to the DSB site. Chromatin-bound RNF8 then cooperates with the E2 conjugating enzyme UBC13 to ubiquitylate H2A-type histones. This ubiquitylation event is opposed by USP3 and USP16. Note that RNF8 interacts with the E3 ubiquitin ligase HERC2, which likely acts to stabilize the RNF8/UBC13 interaction. (b) Ubiquitylated H2A-type histones are recognized by the E3 ubiquitin ligase RNF168, which then interacts with UBC13 to amplify RNF8-dependent histone ubiquitylation and to catalyze the addition of UbK63 conjugates onto other yet unknown substrates (denoted as “X”). RNF168/UBC13-mediated ubiquitylation is counteracted by OTUB1. (c) RNF8/RNF168-mediated regulatory ubiquitylation in the vicinity of DSBs is critical for the sustained recruitment of downstream checkpoint and repair proteins including BRCA1 and RAD18 (two additional E3 ubiquitin ligases) and 53BP1. BRCC36 is a BRCA1-associated DUB that also counteracts this pathway. See text for details. Ub, ubiquitin; P, phosphorylated residue; Me, methyl group.