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Human Exonuclease 1 (EXO1) Regulatory Functions in DNA Replication with Putative Roles in Cancer

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Human Exonuclease 1 (EXO1) Regulatory Functions in DNA Replication with Putative Roles in Cancer International Journal of Molecular Sciences Review Human Exonuclease 1 (EXO1) Regulatory Functions in DNA Replication with Putative Roles in Cancer Guido Keijzers 1,* , Daniela Bakula 1, Michael Angelo Petr 1,2, Nils Gedsig Kirkelund Madsen 1, Amanuel Teklu 1, Garik Mkrtchyan 1, Brenna Osborne 1 and Morten Scheibye-Knudsen 1 1 Department of Cellular and Molecular Medicine, Center for Healthy Aging, University of Copenhagen, DK-2200 Copenhagen, Denmark; [email protected] (D.B.); [email protected] (M.A.P.); [email protected] (N.G.K.M.); [email protected] (A.T.); [email protected] (G.M.); [email protected] (B.O.); [email protected] (M.S.-K.) 2 Experimental Gerontology Section, Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD 21224, USA * Correspondence: [email protected]; Tel.: +45-29-17-65-32 Received: 20 November 2018; Accepted: 19 December 2018; Published: 25 December 2018 Abstract: Human exonuclease 1 (EXO1), a 50!30 exonuclease, contributes to the regulation of the cell cycle checkpoints, replication fork maintenance, and post replicative DNA repair pathways. These processes are required for the resolution of stalled or blocked DNA replication that can lead to replication stress and potential collapse of the replication fork. Failure to restart the DNA replication process can result in double-strand breaks, cell-cycle arrest, cell death, or cellular transformation. In this review, we summarize the involvement of EXO1 in the replication, DNA repair pathways, cell cycle checkpoints, and the link between EXO1 and cancer. Keywords: DNA repair; double strand break repair; exonuclease 1; EXO1; mismatch repair; MMR; NER; nucleotide excision repair; strand displacements; TLS; translesion DNA synthesis 1. Introduction Human exonuclease 1 (EXO1) contributes to checkpoint progression and to several DNA repair pathways involved in reducing DNA replication stress, for example, in mismatch repair (MMR), translesion DNA synthesis (TLS), nucleotide excision repair (NER), double-strand break repair (DSBR), and checkpoint activation to restart stalled DNA forks [1–6]. The multifarious and crucial roles of EXO1 in these DNA repair pathways are summarized in Figure1. EXO1 is a member of the Rad2/XPG family of nucleases [7], and contains an active domain, located at the N-terminal region of the protein (Figure2). The EXO1 transcript has 5 0!30 exonuclease activity, as well as 50 structure specific DNA endonuclease activity and 50!30 RNase H activity [7,8]. EXO1 has a high affinity for processing double stranded DNA (dsDNA), DNA nicks, gaps, and DNA fork structures, and is involved in resolving double Holliday junctions [9–12]. During DNA replication in the S-phase of the cell cycle, a polymerase can incorporate a mismatched DNA base or encounter secondary DNA structures, which can stall the replication fork and lead to replication stress. The collapse of a replication fork can have severe consequences, and failure to restart a stalled fork may lead to double-strand breaks, chromosomal rearrangement, cell-cycle arrest, cell death, or malignant transformation [13,14]. The contribution of EXO1 in the safeguarding stability of the genome during DNA replicative and post-replicative processes is well-established. EXO1 activity contributes to several DNA repair processes; however, it is not clear if the absence or malfunction of EXO1 can contribute to cancer Int. J. Mol. Sci. 2019, 20, 74; doi:10.3390/ijms20010074 www.mdpi.com/journal/ijms Int. J. Mol. Sci. 2019, 20, 74 2 of 15 development. We will herein examine the putative wider roles of EXO1 as a guardian of our genome Int. J. Mol. Sci. 2019, 20, x FOR PEER REVIEW 2 of 15 Int.and J. investigateMol. Sci. 2019, its20, possiblex FOR PEER role REVIEW in cancer progression and initiation. 2 of 15 Figure 1. Human EXO1 participates in both replicative and post-replicative processes. In the Figure 1. HumanHuman EXO1 EXO1 participates participates in both replicativereplicative andand post-replicativepost-replicative processes.processes. In the replicative process, EXO1 contributes to DNA replication by assisting in the removal of mismatches, replicative process, EXO1 contributes to to DNA DNA replic replicationation by by assisting assisting in in the the removal removal of of mismatches, mismatches, bypassing the lesion using translesion synthesis, or by assisting with nucleotide excision repair by bypassing the lesion using translesion synthesis, or by assisting with nucleotide excision repair by activating the NER repair pathway. EXO1 also has a role in DNA resection during the process of activating the NER repair pathway. EXO1 EXO1 also also ha hass a a role in DNA resection during the process of homologous recombination. homologous recombination. FigureFigure 2. 2. InteractionInteraction domains domains in EXO1. in EXO1. Schematic Schematic overview overview of the of relevant the relevant interaction interaction domains domains in the Figure 2. Interaction domains in EXO1. Schematic overview of the relevant interaction domains in the humanin the humanEXO1 protein, EXO1 protein, denoting denoting interaction interaction domains domains with mismatch with mismatch repair proteins repair proteinsMSH3, MLH1, MSH3, human EXO1 protein, denoting interaction domains with mismatch repair proteins MSH3, MLH1, MSH2,MLH1, MSH2,and other and significant other significant interaction interaction regions, regions, including including with with PARP1, PARP1, PCNA, PCNA, and and the the nuclear nuclear MSH2, and other significant interaction regions, including with PARP1, PCNA, and the nuclear localizationlocalization signal signal (NLS). (NLS). localization signal (NLS). 2.2. DNA DNA Replication Replication 2. DNA Replication EnzymesEnzymes able able to to metabolize metabolize DNA DNA are are required required for for modulating modulating DNA DNA replication. replication. EXO1 EXO1 is Enzymes able to metabolize DNA are required for modulating DNA replication. EXO1 is intricatelyis intricately involved involved in this in thisprocess process both bothas an as enzyme an enzyme involved involved in replication in replication and in andDNA in repair DNA intricately involved in this process both as an enzyme involved in replication and in DNA repair pathwaysrepair pathways such as suchhomologous as homologous recombination, recombination, but it is also but an it isessential also an enzyme essential in enzymethe replication in the pathways such as homologous recombination, but it is also an essential enzyme in the replication process,replication such process, as DNA such strand as DNA displacement. strand displacement. Strand displacement Strand displacement describes the describes removal the of removal single process, such as DNA strand displacement. Strand displacement describes the removal of single strandedof single RNA stranded or DNA RNA from or DNA an RNA:DNA from an RNA:DNA or DNA:DNA or DNA:DNA duplex, a duplex,process arequired process for required multiple for stranded RNA or DNA from an RNA:DNA or DNA:DNA duplex, a process required for multiple essentialmultiple cellular essential processes, cellular processes,such as DNA such replicat as DNAion replication and DNA andrepair. DNA Accordingly, repair. Accordingly, flap structure- flap essential cellular processes, such as DNA replication and DNA repair. Accordingly, flap structure- specificstructure-specific endonuclease endonuclease 1 (FEN1), EXO1, 1 (FEN1), and polymerase EXO1, and polymeraseδ are the mainδ are factors the mainin primer factors removal in primer and specific endonuclease 1 (FEN1), EXO1, and polymerase δ are the main factors in primer removal and Okazakiremoval andfragment Okazaki maturation fragment at maturation the lagging at thestrand lagging in the strand process in the of process strand of displacement strand displacement during Okazaki fragment maturation at the lagging strand in the process of strand displacement during replicationduring replication [8,15–19]. [8, 15In– yeast,19]. In EXO1 yeast, can EXO1 substitu can substitutete for RAD27 for RAD27 (FEN1 (FEN1is the human is the human homolog) homolog) in RNA in replication [8,15–19]. In yeast, EXO1 can substitute for RAD27 (FEN1 is the human homolog) in RNA primer removal [11]. Indeed, in vitro assays suggest that 5’ flaps (< 5 nt) generated by polymerase δ primer removal [11]. Indeed, in vitro assays suggest that 5’ flaps (< 5 nt) generated by polymerase δ during replication are efficiently removed by FEN1 or EXO1 [9,11,15,16]. The 3’-exonuclease activity during replication are efficiently removed by FEN1 or EXO1 [9,11,15,16]. The 3’-exonuclease activity of polymerase δ avoids excessive strand displacement [19]. Deletion of POL32 (third subunit of of polymerase δ avoids excessive strand displacement [19]. Deletion of POL32 (third subunit of polymerase δ) can suppress the lethality of growth defects of RAD27 and polymerase δ D520V polymerase δ) can suppress the lethality of growth defects of RAD27 and polymerase δ D520V Int. J. Mol. Sci. 2019, 20, 74 3 of 15 RNA primer removal [11]. Indeed, in vitro assays suggest that 5’ flaps (<5 nt) generated by polymerase δ during replication are efficiently removed by FEN1 or EXO1 [9,11,15,16]. The 3’-exonuclease activity of polymerase δ avoids excessive strand displacement [19]. Deletion of POL32 (third subunit of polymerase δ) can suppress the lethality of growth defects of RAD27 and polymerase δ D520V mutants in yeast (defective for RAD27 and the 3’!5’ exonuclease of polymerase δ)[20]. In support of this
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