Replication-associated base excision repair Of oxidized bases in the mammalian genome

Reactive oxygen species (ROS), the most pervasive endogenous and radiation-induced genotoxic agents induce strand breaks and a plethora of base lesions in DNA that (except double-strand breaks) are repaired via the DNA base excision repair (BER) pathway. Four mammalian DNA glycosylases, namely, OGG1 and NTH1 in the Nth family, and NEIL1 and NEIL2 in the Nei family, with overlapping substrate range initiate BER by excising oxidized base lesions and cleaving the DNA strand. NEIL1 prefers oxidized pyrimidines or ring-opened purines as substrates and is upregulated at the mRNA and protein level during S-phase. NEIL1 also demonstrates the unique able to excise base lesions from forked or single-stranded DNA substrates that mimic intermediates generated during DNA replication. This suggests a direct linkage of NEIL1’s repair activity to genome replication. In addition, inactivating mutations in the NEIL1 gene have been epidemiologically linked with gastric cancer, NEIL1-downregulation induces a mutator phenotype and NEIL1 KO mice display symptoms of the human metabolic syndrome such as obesity, dyslipidemia, and fatty liver disease. These observations lead us to develop the working hypothesis that NEIL1 is involved in a preferential repair pathway for oxidized base damage in the replicating genome where repair of both template strands is equally important because an unrepaired base lesion in either strand could induce mutations. Thus, specific involvement of NEIL1 with the DNA replication machinery may be required to effectively and efficiently accomplish this. In support of our hypothesis, we have identified several new NEIL1 interacting proteins that are components of the DNA replication machinery, including Replication Protein A (RPA), Proliferating Cell Nuclear Antigen (PCNA), Flap Endonuclease 1 (FEN1), DNA Polymerase ä, Replication Factor C (RFC), and DNA Ligase I as well as the stress responsive Rad9-Rad1-Hus1 (9-1-1) DNA sliding clamp. We mapped the overlapping binding sites for all of these interacting protein partners to a small disordered region near the unconserved C-terminus of NEIL1 that is dispensable for its enzymatic activity. In support of the biological significance of these interactions, we showed that the DNA polymerase processivity factor and sliding clamp, PCNA, stimulates NEIL1’s activity on various DNA substrates including forked and single-stranded DNA. We also investigated NEIL1’s association with the DNA damage activated alternative sliding clamp 9-1-1 and showed direct interaction as well as stimulation of NEIL1 activity in a similar fashion as PCNA. In contrast, the RPA complex inhibits NEIL1’s activity when the damage is in the single-stranded region of a DNA primer-template structure, inhibition that is relieved in the presence of PCNA. These results suggest that PCNA and RPA, along with other proteins, collaborate to regulate a replication-associated repair pathway in mammalian cells that not only maintains efficient and proper replication but also repair of oxidative DNA damage to prevent mutagenesis and maintain genomic integrity.