Timely upstream events regulating nucleotide excision repair by ubiquitin-proteasome system: ubiquitin guides the way

Abstract

The ubiquitin-proteasome system (UPS) plays crucial roles in regulation of multiple DNA repair pathways, including nucleotide excision repair (NER), which eliminates a broad variety of helix-distorting DNA lesions that can otherwise cause deleterious mutations and genomic instability. In mammalian NER, DNA damage sensors, DDB and XPC acting in global genomic NER (GG-NER), and, CSB and RNAPII acting in transcription-coupled NER (TC-NER) sub-pathways, undergo an array of post-translational ubiquitination at the DNA lesion sites. Accumulating evidence indicates that ubiquitination orchestrates the productive assembly of NER preincision complex by driving well-timed compositional changes in DNA damage-assembled sensor complexes. Conversely, the deubiquitination is also intimately involved in regulating the damage sensing aftermath, via removal of degradative ubiquitin modification on XPC and CSB to prevent their proteolysis for the factor recycling. This review summaries the relevant research efforts and latest findings in our understanding of ubiquitin-mediated regulation of NER and active participation by new regulators of NER, e.g., Cullin-Ring ubiquitin ligases (CRLs), ubiquitin-specific proteases (USPs) and ubiquitin-dependent segregase, valosin-containing protein (VCP)/p97. We project hypothetical step-by-step models in which VCP/p97-mediated timely extraction of damage sensors is integral to overall productive NER. The USPs and proteasome subtly counteract in fine-tuning the vital stability and function of NER damage sensors.

Keywords: Nucleotide excision repair; Ultraviolet radiation; deubiquitination; ubiquitination.

Figure 1.

Hypothetical model depicting sequential steps in the assembly of preincision complex in GG-NER. In damage recognition step, CRL^DDB2 is recruited to DNA lesions in chromatin and its E3 activity is activated upon binding to lesion-situated DNA strand, leading to K48-linked ubiquitination of DDB2. The CRL^DDB2 binding consequently reveals the DNA bubble, recruits XPC to bind to DNA strand opposite the lesion, directs E3 activity towards XPC and leads to K48-linked ubiquitination of XPC. In damage verification step, XPC, with enhanced damage binding due to specific ubiquitination, recruits TFIIH. The K48-polyubiquitinated DDB2 is extracted by VCP/p97, stabilizing the binding of XPC as well as TFIIH upon detaching of its CAK complex. Lodging of core TFIIH further promotes DDB2 dissociation and XPA binding, forming a stable ternary XPC-TFIIH-XPA damage verification complex. The RNF111 is recruited and mediates SUMO-targeted K63-ubiquitination of XPC. Subsequently, VCP/p97 mediates ubiquitin-dependent extraction of both K48- and K63-ubiquitinated XPC from DNA lesion sites. USP11 may be recruited to ubiquitinated XPC to trim down K63-ubiquitin chains to optimize the transient XPC retention. The departure of XPC in turn facilitates the arrival of XPG, XPF and RPA, forming the final preincision complex. The ubiquitinated DDB2 undergoes proteolysis. Whereas, the K48-ubiquitinated XPC is deubiquitinated by USP7, which restores the native state of XPC in cell.

Figure 2.

Hypothetical model depicting the assembly of preincision complex in TC-NER. The CSB checks on transcription elongation by continuously probing RNAPII-containing elongating complex. When bulky lesion blocks transcription by stalling elongating RNAPII, CSB immobilizes on stalled elongating RNAPII, forming a stable RNAPII-CSB complex, which functions as damage sensor. The RNAPII-CSB complex recruits Cullin-Ring ligase(s) (CRLs) and CRL4^CSA to ubiquitinate RNAPII at K1268 and CSB, respectively. UVSSA is recruited by CSB and CSA, perhaps in the form of UVSSA-USP7 complex. The UVSSA is mono-ubiquitinated at K414 and in turn recruits TFIIH via binding to the PH domain of p62 subunit of TFIIH and transfers TFIIH to RNAPII. The ubiquitinated RNAPII and CSB are extracted by VCP/p97 complex, causing the departure of CRLs and other factors inessential to TC-NER and promoting the formation of DNA damage UVSSA-TFIIH-XPA verification complex. Finally, the arrival of XPG, XPF and RPA and the departure of UVSSA complete the formation of preincision complex. The ubiquitinated CSB undergoes deubiquitination by USP7, whereas ubiquitinated RNAPII is degraded by proteasome.