Inhibition of abasic site cleavage in bubble DNA by multifunctional protein YB-1 Elizaveta E. Fomina a , Pavel E. Pestryakov a , Dmitry A. Kretov b,c , Dmitry O. Zharkov a,d , Lev P. Ovchinnikov c , Patrick A. Curmi b and Olga I. Lavrik a,d,e * Y-box binding protein 1 (YB-1) is widely known to participate in a multiple DNA and RNA processing events in the living cell. YB-1 is also regarded as a putative component of DNA repair. This possibility is supported by relocalization of YB-1 into the nucleus following genotoxic stress. Increased affinity of YB-1 for damaged DNA, especially in its single- stranded form, and its functional interaction with proteins responsible for the initiation of apurinic/apyrimidinic (AP) site repair, namely, AP endonuclease 1 and DNA glycosylase NEIL1, suggest that YB-1 could be involved in the repair of AP sites as a regulatory protein. Here we show that YB-1 has a significant inhibitory effect on the cleavage of AP sites located in single-stranded DNA and in DNA bubble structures. Such interference may be considered as a possible mechanism to prevent single-stranded intermediates of DNA replication, transcription and repair from being converted into highly genotoxic DNA strand breaks, thus allowing the cell to coordinate different DNA processing mechanisms. Copyright © 2015 John Wiley & Sons, Ltd. Keywords: AP endonuclease 1 (APE1); NEIL1; Y-box binding protein 1 (YB-1); DNA repair; abasic site (AP site) INTRODUCTION The easiness of coding base loss experienced by DNA of mammalian cell (roughly 10 4 –10 5 events per cell per day) is surprising given the significant cytotoxicity of the resulting lesions—apurinic/ apyrimidinic (abasic, AP) sites (Wilson and Barsky, 2001). AP sites are chemically unstable, representing a major source of single- strand DNA breaks and also a source of protein-DNA crosslinks (Sczepanski et al., 2010; Müller et al., 2013). The absence of a coding base in a DNA template results in either blocking the activities of DNA and RNA polymerases or base substitutions and deletions if DNA translesion synthesis goes on. In living cells, AP sites are repaired by at least two pathways. The “classic” pathway utilizes the base excision repair (BER) machinery and is initiated by the hydrolysis of the damaged DNA strand by AP endonuclease 1 (APE1) (Wilson and Barsky, 2001). The “backup” pathway starts from cleavage of lesion-containing strand by bifunctional DNA glycosylases, which have an associated AP lyase activity (Hazra et al., 2007). Notably, several enzymes of the latter pathway (e.g. human endonuclease VIII-like proteins NEIL1 and NEIL2) show preference for lesions located in partly single-stranded DNA (Dou et al., 2003; Hegde et al., 2008). Despite the importance of rapid elimination of potentially mutagenic lesions such as AP sites, an immediate start of BER is not always of implicit advantage. Genomic DNA is involved in a number of dynamic processes; thus, AP sites may emerge in intermediates of DNA replication, transcription, etc., and may be localized in the single-stranded DNA fragments transiently present during these processes. If AP site repair starts in such an intermediate, the cleavage of AP site containing strand may result in unfavorable double-stranded DNA breaks (DSB). The repair of DSB is complex and frequently leads to a loss of genetic material (Jackson, 2001). Nevertheless, there is evidence for in vitro ligation of DNA strands after NEIL1-catalyzed release of damaged nucleotide located in an unwound region of DNA (Zhao et al., 2010). In living cells, such scenario would lead to single-nucleotide dele- tions and frameshift mutations. This implies that the absence of the complementary strand opposite the AP site would require mechanisms for specific regulation of the excision of this lesion to disfavor mutagenic repair by the backup pathway. Multifunctional Y-box binding protein 1 (YB-1) localizes primarily in the cytoplasm of eukaryotic cells (Lasham et al., 2003; En-Nia et al., 2005); however, under genotoxic stress, large amounts of * Correspondence to: Olga I. Lavrik, Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia. E-mail: lavrik@niboch.nsc.ru a E. E. Fomina, P. E. Pestryakov, D. O. Zharkov, O. I. Lavrik Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia b D. A. Kretov, P. A. Curmi Laboratoire Structure-Activité des Biomolécules Normales et Pathologiques, Institut National de la Santé et de la Recherche Médicale (INSERM), UMR829, Université Evry-Val d’Essonne, Evry, France c D. A. Kretov, L. P. Ovchinnikov Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow region, 142290, Russia d D. O. Zharkov, O. I. Lavrik Novosibirsk State University, Novosibirsk 630090, Russia e O. I. Lavrik Altai State University, Barnaul 656049, Russia Abbreviations: YB-1, Y-box binding protein 1; AP site, apurinic/apyrimidinic, abasic site; APE1, AP endonuclease 1; BER, base excision repair; dsDNA, double- stranded DNA; ssDNA, single-stranded DNA. Research Article Received: 22 May 2014, Revised: 11 September 2014, Accepted: 13 September 2014, Published online in Wiley Online Library: 2014 (wileyonlinelibrary.com) DOI: 10.1002/jmr.2435 J. Mol. Recognit. (2015) Copyright © 2015 John Wiley & Sons, Ltd.