Using molecular, biochemical and structural approaches, we have broadly contributed to defining how specific human BER proteins recognize and process target lesions, as well as coordinate with other components of the protective system. The research has centered largely on apurinic/apyrimidinic endonuclease 1 (APE1), the major mammalian protein for repairing abasic sites in DNA, and x-ray cross-complementing 1 (XRCC1), a non-enzymatic scaffold protein that facilitates the efficient execution of single-strand break (SSB) repair. Some of the key findings during the course of the project include: (i) in addition to abasic sites in conventional duplex DNA, APE1 has the ability to incise at AP sites in DNA conformations formed during DNA replication, transcription, and class switch recombination, and APE1 can endonucleolytically destroy damaged RNA; (ii) APE1 contributes to the repair of 3-modifications in DNA, such as mismatches, phosphate groups, phosphogycolates and tyrosyl residues; (iii) the DNA repair function of APE1 is regulated in part by post-translational modification, such as S-glutathionylation; (iv) inhibition of APE1 is a potential mechanism for the genotoxic and co-carcinogenic effects of lead, an important environmental toxin; (v) APE1 communicates with CSB, a protein defective in the premature aging disorder, Cockayne syndrome; (vi) XRCC1 directly associates with the replication/repair protein, PCNA, establishing a novel link between the DNA repair machinery and replication factories; (vii) XRCC1 coordinates disparate responses and multi-protein repair complexes that are dependent on the nature and context of the DNA damage; (viii) the different regions of XRCC1 play distinct roles in coordinating repair complex assembly, and the population variant Arg280His exhibits reduced stability at DNA damage foci, suggesting that it may represent a disease susceptibility factor; (ix) XRCC1 supports an emerging pathway for uracil repair, termed replication-associated BER, through a physical association with UNG2, the major nuclear uracil DNA glycosylase; (x) the interaction of XRCC1 with the DNA repair enzyme PNKP functions to retain XRCC1 at DNA damage sites and to promote repair of alkylation damage; (xi) the flap-endonuclease FEN1 plays a role in repairing mitochondrial oxidative DNA damage through a long-patch BER pathway; (xii) RECQL4, a human RecQ helicase mutated in approximately two-thirds of individuals with Rothmund-Thomson syndrome, regulates BER capacity both directly and indirectly; and (xiii) RECQL5, another RECQ helicase family member, modulates and/or directly participates in BER of endogenous DNA damage, thereby promoting chromosome stability in normal human cells. Our most recent work has demonstrated that (i) the DNA glycosylase NEIL1 recognizes specifically ICLs in DNA, and can obstruct the efficient removal of these lethal lesions; (ii) the multifunctional protein nucleophosmin (a.k.a., NPM1) is a modulator of BER capacity by controlling BER protein levels and regulating the nucleolar localization of several BER enzymes; (iii) the efficiency of APE1 binding and strand incision are influenced by the domain sequence, conformation and AP site location/relative positioning within telomeric and CAG/CTG repeat sequences; and (iv) specific APE1 variants (e.g., the tumor-associated R237C variant) are uniquely hypersensitive to nucleosome complexes in the vicinity of the AP site, suggesting the evolution of distinct surface residues that permit efficient processing of abasic sites within the context of protein-DNA complexes independent of classic chromatin remodeling mechanisms. Currently, a main focus is to establish genetically modified cell lines to dissect out the precise contribution of each proposed function of APE1 (i.e. its nuclease activity, redox regulatory role, etc.) in cell growth/viability, genome maintenance, and protection against DNA-damaging agents. Defining which of the many reported functions of APE1 are critical to normal cellular activity is a key step towards understanding the potential relationship of the protein to the aging process and disease risk.
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