The N-terminal domain of uracil-DNA glycosylase: Roles for disordered regions

Abstract

The presence of uracil in DNA calls for rapid removal facilitated by the uracil-DNA glycosylase superfamily of enzymes, which initiates the base excision repair (BER) pathway. In humans, uracil excision is accomplished primarily by the human uracil-DNA glycosylase (hUNG) enzymes. In addition to BER, hUNG enzymes play a key role in somatic hypermutation to generate antibody diversity. hUNG has several isoforms, with hUNG1 and hUNG2 being the two major isoforms. Both isoforms contain disordered N-terminal domains, which are responsible for a wide range of functions, with minimal direct impact on catalytic efficiency. Subcellular localization of hUNG enzymes is directed by differing N-terminal sequences, with hUNG1 dedicated to mitochondria and hUNG2 dedicated to the nucleus. An alternative isoform of hUNG1 has also been identified to localize to the nucleus in mouse and human cell models. Furthermore, hUNG2 has been observed at replication forks performing both pre-and postreplicative uracil excision to maintain genomic integrity. Replication protein A (RPA) and proliferating cell nuclear antigen (PCNA) are responsible for recruitment to replication forks via protein-protein interactions with the N-terminus of hUNG2. These interactions, along with protein degradation, are regulated by various post-translational modifications within the Nterminal tail, which are primarily cellcycle dependent. Finally, translocation on DNA is also mediated by interactions between the N-terminus and DNA, which is enhanced under molecular crowding conditions by preventing diffusion events and compacting tail residues. This review summarizes recent research supporting the emerging roles of the N-terminal domain of hUNG.

Identification of a Chemotherapeutic Lead Molecule for the Potential Disruption of the FAM72A-UNG2 Interaction to Interfere with Genome Stability, Centromere Formation, and Genome Editing

“…The UNG2 protein can be functionally divided into two domains: an N-terminal regulatory region (AA 1–92) and a C-terminal catalytic region (AA 93–313). The disordered N-terminal region has been identified as interacting with several proteins, including proliferating cell nuclear antigen (PCNA) and replication protein A (RPA) (both found at DNA replication forks), as well as with FAM72A [ 2 , 16 , 17 , 18 , 26 , 27 ]. To further enlighten the FAM72A-UNG2 interaction, we investigated the N-terminus of UNG2 (AA 1–92), applying the Modeller, I-TASSER, and AlphaFold protein structure prediction analysis programs.…”

“…The FAM72A monomer was exported as a PDB file (FAM72A 3D protein structure was used from previously designed PDB data [ 30 ]), whereas the UNG2 (AA 1–45) peptide was submitted as a FASTA-formatted AA sequence (AA 1–45). The UNG2 (AA 1–45) peptide was used because these AAs appeared to be the pivotal interacting AAs [ 2 , 16 , 17 , 18 , 26 ]. The docked structure was analyzed for specific AAs contributing to the FAM72A protein and UNG2 peptide interactions.…”

“…The N-terminal regulatory region of UNG2 is described as an intrinsically disordered region by several groups [ 16 , 17 , 42 ]. In continuation, JPred4 [ 43 ] was used for additional secondary structure prediction.…”

“…Amino acid (AA) residues 1–92 make up the N-terminus of UNG2; they contain a nuclear localization signal of positively charged residue clusters (K and R residues), rendering UNG2 as the primary uracil-DNA glycosylase enzyme in the nucleus [ 14 , 15 ]. Interestingly, in the absence of binding partners, the N-terminal region is, for the most part, without a fixed structure [ 2 , 16 , 17 , 18 ]. UNG2 is rapidly recruited to sites of DNA damage where its N-terminus can interact with its catalytic site (which binds to uracil) and with chromatin.…”

Recruitment of ubiquitin E2 enzymes is determined jointly by the U‐box domains and substrates of E3 ligases

“…PYCR2 is a mitochondrial enzyme that serves as a prognostic biomarker for subgrouping and metabolic reprogramming in hepatocellular carcinoma (HCC) [36]. Uracil DNA glycosylase (UNG) is a DNA glycosylase involved in DNA repair through the uracil base excision repair process [37]. As a specific substrate shared by CHIP and E4B [28], PRMT1 (Protein arginine N ‐methyltransferase 1) is capable of catalyzing the monomethylation and asymmetric dimethylation of arginine residues in proteins and participates in the development of embryos, DNA damage repair, and progression of diverse cancers [38].…”