**1. Introduction**

Many forms of DNA damage are generated due to permanent action of endogenous and exogenous factors. In order to maintain genome integrity, cells have evolved several specific pathways to repair DNA lesions. Base excision repair (BER), which ensures correction of the most abundant damages—modified nitrogenous bases and apurinic/apyrimidinic (AP) sites—is critically important for survival of human cells [1–3]. Enzyme and protein factors of BER also participate in the repair of DNA single-strand breaks (SSBs) considered as a separate pathway of the BER system [4, 5]. The other repair systems (**Figure 1**) deal with bulky nucleobase lesions (NER), DNA double-strand breaks (HR; NHEJ), and mismatched bases (MMR). Impaired DNA repair is associated with embryonic lethality, rapid aging, and a variety of severe human hereditary diseases as well as development of cancer [7, 8]. The balance of DNA damage and DNA repair is highly relevant to both

#### **Figure 1.**

*DNA damages generated by endogenous and exogenous factors and specific systems of their repair. Letter X in DNA duplex marks mismatched base pair. Reproduced with modification from [6] with permission of Pleiades Publishing, Ltd.* 

cancerogenesis and effective anti-cancer therapy due to the ability of cancer cells to repair therapeutically induced DNA damage and impact therapeutic efficacy [9]. Hence, intensive investigation of DNA damage repair is essential to advance our understanding of molecular mechanisms maintaining genome integrity and to develop cancer therapy.

## **2. Main steps of BER and proteins involved**

 The widely accepted model for mammalian BER involves several sub-pathways presented schematically in **Figure 2**. The damaged bases are removed by DNA glycosylases specific to the certain type of damage; mono- and bifunctional DNA glycosylases form an intact or cleaved (via β- or β/δ-elimination mechanism) AP site, respectively [10]. The intact AP site is further processed by the main enzymatic activity of multifunctional AP endonuclease 1 (APE1) producing the one-nucleotide gap with 3′-hydroxyl and 5′-deoxyribose phosphate residue (5′-dRp) at the gap margins. Terminal blocking groups in the DNA intermediates produced by bifunctional DNA glycosylases are removed by the phosphatase activity of polynucleotide kinase/phosphatase (PNKP) or 3′-phosphodiesterase and 3′-phosphatase activities of APE1. At the next step, a bifunctional DNA polymerase β (Polβ) catalyzes the removal of the 5′-dRp residue by its dRp-lyase activity and one-nucleotide gap filling by the nucleotidyl transferase activity. The repair of DNA chain integrity via joining of the single-strand break is completed by DNA ligase IIIα (LigIIIα) acting in the complex with X-ray repair cross-complementing protein 1 (XRCC1). This main BER sub-pathway is known as a short-patch repair (SP BER). When the 5′-dRp residue is modified, it cannot be removed by the Polβ-lyase activity, and a long-patch sub-pathway of BER (LP BER) is realized. Polβ initiates the DNA strand displacement synthesis continued by replicative DNA polymerases δ and ε (Polδ and Polε) acting in the complexes with protein factors PCNA and RFC. The flap structure produced at this step is removed by the flap endonuclease 1 (FEN1). According to another model, FEN1 is capable of sequential removing nucleotides at the 5′-end of the break, and the produced gap is filled by the activities of Polβ or

*Coordination of DNA Base Excision Repair by Protein-Protein Interactions DOI: http://dx.doi.org/10.5772/intechopen.82642* 

**Figure 2.** 

*BER sub-pathways for repair of damaged bases and DNA SSBs. Catalytic steps and proteins involved are schematically presented. The terminal groups in DNA intermediates and SSBs are designated as follows: PUA, 3′-phospho-α,β-unsaturated aldehyde; p, 3′−/5′-phosphate; OH, 3′−/5′-hydroxyl; dRP, 5′-deoxyribose phosphate; PG, 3′-phosphoglycolate; Ade, 5′-aldehyde group; and AMP, 5′-AMP. Reproduced with modification from [6] with permission of Pleiades Publishing, Ltd.* 

Polλ [11, 12]. Final ligation of the break is catalyzed by DNA ligase I (LigI). A new long-patch sub-pathway of BER that involves formation of a 9-nucleotide gap 5′ to the lesion has been recently discovered; it is mediated by DNA helicase RECQ1 and ERCC1-XPF endonuclease in cooperation with PARP1 and replication protein A (RPA) [13].

Repair of DNA SSBs arising directly via disintegration of the oxidized sugar and as a result of erroneous activity of DNA topoisomerase 1 involves the following steps: (1) detection of the break, (2) removal of blocking groups, (3) filling the gap, and (4) ligation of the break (**Figure 2**). The DNA breaks are detected primarily by poly(ADP-ribose) polymerase 1 (PARP1); the unblocking of 3′- and 5′-ends in breaks is catalyzed by specific activities of APE1, PNKP, aprataxin (APTX), and tyrosyl-DNA phosphodiesterase 1 (TDP1); gap filling and ligation are catalyzed by the same set of enzymes that participate in the respective steps of the short-patch repair of the damaged DNA bases (Polβ and LigIIIα). PARP1 is activated via the interaction with the damaged DNA; it catalyzes the synthesis of poly(ADP-ribose) (PAR) and covalent attachment of the PAR polymer to PARP1 itself and other proteins involved in the DNA repair [4, 5]. The XRCC1 protein is considered to be a main target of PARP1 catalyzed poly(ADP-ribosyl)ation. PARP1 has been suggested to play the main role in recruitment of the XRCC1 protein to the damages of chromosomal DNA [4, 5]. XRCC1 displays no enzymatic activity and is proposed to function as a scaffold protein of the BER process. PARP2 is another enzyme from the PARP family that is activated via binding with DNA SSB and catalyzes PAR

synthesis [14, 15]. The importance of both PARP1 and PARP2 for DNA repair is indicated by knockout studies revealed that knocking out the *parp1* gene activity increased the sensitivity of cells to DNA-damaging agents, while *parp1* and *parp2* double knockouts caused early embryonic lethality [16]. The role of PARP2 in BER processes and its possible synergism with PARP1 action are under intensive investigation [17, 18]. Poly(ADP-ribosyl)ation of proteins is a transient modification that turns over rapidly due to the enzymatic activity of poly(ADP-ribose) glycohydrolase (PARG) [19]. Another important function of PARP1 in DNA repair is remodeling of chromatin structure via poly(ADP-ribosyl)ation of histones and binding of the remodeling proteins with the synthesized PAR polymer [20].

Coordinated action of the enzymes catalyzing the sequential individual reactions of the multistep BER process is required for efficient repair of damaged DNA. One of the coordination mechanisms proposed previously is the "passing the baton," that implies the transfer of the DNA intermediate from the enzyme remaining bound to the product to the next enzyme [1, 21]. This model is supported by numerous data on mutual modulation of activities of the BER enzymes [2, 21]. The stimulating effect of APE1 on the catalytic activity of DNA glycosylase OGG1 explored in detail recently does not require direct interaction between the proteins and is adequately described by the "passing the baton" model [22]. Another mechanism of coordination implies the formation of multiprotein complexes (so-called repairosomes) composed of enzymes and scaffold proteins [2]. XRCC1 is a striking example of the scaffold protein involved in BER. The existence of "repairosomes" is evidenced by multiple interactions between enzymes and protein factors of BER detected even independent of the DNA damage. Most likely both mechanisms are relevant to coordination of the BER process.
