Living on the Edge: DNA Polymerase Lambda between Genome

Review Cite This: Chem. Res. Toxicol. 2017, 30, 1936-1941

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Living on the Edge: DNA Polymerase Lambda between Genome Stability and Mutagenesis Barbara van Loon,§,⊥ Ulrich Hübscher,‡ and Giovanni Maga*,† †

DNA Enzymology & Molecular Virology and Cell Nucleus & DNA replication Units, Institute of Molecular Genetics IGM-CNR, via Abbiategrasso 207, I-27100 Pavia, Italy ‡ Department of Molecular Mechanisms of Disease, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland § Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Erling Skjalgssons gt 1, N-7491 Trondheim, Norway ⊥ Department of Pathology and Medical Genetics, St. Olavs Hospital, Trondheim University Hospital, 7491 Trondheim, Norway ABSTRACT: In human cells, only four DNA polymerases (pols) are necessary and sufficient for the duplication of the genetic information. However, more than a dozen DNA pols are required to maintain its integrity. Such a high degree of specialization makes DNA repair pols able to cope with specific lesions or repair pathways. On the other hand, the same DNA pols can have partially overlapping roles, which could result in possible conflicts of functions, if the DNA pols are not properly regulated. DNA pol λ is a typical example of such an enzyme. It is a multifunctional enzyme, endowed with special structural and biochemical properties, which make it capable of participating in different DNA repair pathways such as base excision repair, nonhomologous end joining, and translesion synthesis. However, when mutated or deregulated, DNA pol λ can also be a source of genetic instability. Its multiple roles in DNA damage tolerance and its ability in promoting tumor progression make it also a possible target for novel anticancer approaches.

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CONTENTS

1. Introducing DNA Polymerase λ 2. Biochemical Features of DNA Polymerase λ 3. DNA Polymerase λ in Base Excision Repair and Oxidative Damage Response 4. DNA Polymerase λ in Nonhomologous End Joining and Microhomology Mediated End Joining 5. Regulation of DNA Polymerase λ 6. DNA Polymerase λ and Cancer 7. Conclusions Author Information Corresponding Author ORCID Funding Notes Biographies Abbreviations References

similarity, can be grouped into the families A, B, X, Y, AEP, and RT (reviewed in refs 1−3). Appropriate division of labor among these DNA pols is essential to control mutation frequency; indeed, DNA pols are at the heart of almost all DNA repair pathways. One of human DNA pols families is the family X. This family is composed of four specialized DNA pols (β, λ, μ, and TdT), all of which participate in different DNA repair pathways and are involved in the synthesis of short DNA segments.4 In 2000, Luis Blanco reported DNA pol λ as a novel eukaryotic DNA pol with a potential role in meiosis.5 DNA pol λ appears to have important DNA repair functions in different processes such as base excision repair (BER), translesion synthesis (TLS), double-strand break repair (DSBR), and in a physiological homeostasis (for more details, see sections 3 and 4). DNA pol λ is unique among X family members, as it possesses all enzymatic activities associated with this family: DNA polymerization, terminal transferase, dRPlyase, and polynucleotide synthetase. Indeed, beside vertebrates, all other eukaryotic organisms possess only one family X DNA pol, which, based on sequence homology, is the ortholog of DNA pol λ, thus making DNA pol λ the most conserved X-family DNA pol throughout evolution.6,7 Biochemical characterization of DNA pol λ from

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1. INTRODUCING DNA POLYMERASE λ DNA polymerases (pols) are the key enzymes for all DNA synthesis events such as DNA replication and the many different DNA repair events or DNA recombination including V(D)J recombination. So far, 17 different DNA pols are known in mammalian cells, which, based on their amino acid sequence © 2017 American Chemical Society

Special Issue: DNA Polymerases: From Molecular Mechanisms to Human Disease Received: June 5, 2017 Published: August 25, 2017 1936

DOI: 10.1021/acs.chemrestox.7b00152 Chem. Res. Toxicol. 2017, 30, 1936−1941

Chemical Research in Toxicology

Review

Table 1. Biochemical Properties of DNA Pol λa DNA template 1−2 nt DNA gap

a

metal activator Mn2+ > Mg2+

catalytic efficiency (kcat/Km, M−1 s−1) 3′−OH

dNTP

5 × 105

1−3 × 106

error rate

selectivity dNTPs vs rNTPs

lesion bypass (outcome)

1 × 10−3

3000−4000

8-oxo-G (coding) 2-OH-dAb (miscoding) abasic site (−1 frameshift)

Data taken from ref 1. b2-OH-dA, 2-hydroxy-2′-deoxy adenosine.

chain.15 Finally, DNA pol λ can act as a translesion polymerase over a variety of DNA lesions.3 The main biochemical features of DNA pol λ are summarized in Table 1. Several structural studies have helped to clarify the basis for such a remarkable catalytic flexibility of DNA pol λ. A structure of the catalytic domain of DNA pol λ in complex with a gapped DNA substrate16 showed a substantially different architecture of its active site with respect to other DNA pols. DNA pol λ makes fewer interactions with the template strand than family A and B DNA pols, mainly contacting only the 3′ terminal base pair. The N-terminal 8 kDa lyase domain is involved in contacts with the downstream 5′-phosphate. Structures of the ternary complex of DNA pol λ with DNA and an incoming dNTP, also indicated that the active site is in a “closed” conformation even in the absence of a bound dNTP.17 Such a a closed conformation, mediated by a specific N-terminal extension of the 8 kDa domain, was shown to be required for end-bridging during NHEJ.18 DNA pol λ is also able to accommodate bulky purine/purine mismatches in its active site, as shown by structures of the enzyme in complex with a mismatched (G:G) primer/template, providing a rationale for its TLS ability.19 Further crystal structures of DNA pol λ bound to different frameshift intermediates, which revealed that DNA pol λ “scrunches” the template, by accommodating a template base in an extrahelical position within a specific binding pocket.20 This explains the high rate of −1 frameshifts generated by DNA pol λ and points to its ability in elongating aberrant primer ends, such as those containing base lesions, or primer/template pairs with minimal homology, such as those generated during nonhomologous end joining (NHEJ). A series of crystal structures of DNA pol λ trapped in complex with the different intermediates during BER of 8-oxo-G19 showed that in the binary complex, DNA pol λ accommodates the templating 8-oxo-G exclusively in its syn conformation, similarly to what has been observed in the complex with the G:G mismatch.17 However, while the syn conformation is maintained in the ternary complex with dATP, DNA pol λ can allow rotation of the templating 8-oxo-G in the anti conformation when dCTP is present, with minimal perturbations in the architecture of the active site. Extension from a G:G mismatch has been shown to be at least 50-fold less efficient than from a correct G:C basepair.17 Structural studies suggested that this was due to the perturbation of the critical interactions between the primer/template and the Arg517 residue. Such interactions, on the other hand, are maintained in the case of the 8-oxo-G:dAdo mismatch. However, DNA pol λ can strongly discriminate against elongation from a (syn)8-oxoG:dAdo basepair, favoring the (anti)8-oxo-G:dCyt one. The new crystal structures revealed that the anti conformation of 8-oxo-G paired to an incoming dCTP is stabilized by an additional hydrogen bond between Glu259 and the N2-group of the oxidized base. Conversely, such interaction is not possible in the syn conformation due to a steric clash with the C8 carbonyl of 8oxo-G.19 These data explain the high efficiency and fidelity of

Oriza sativa and Arabidopsis thaliana has revealed a remarkable functional similarity of the plant enzymes with their animal cell counterpart including the ability to participate in BER and to bypass abasic sites and 7,8-dihydro-8-oxoguanine (8-oxo-G).8,9 Remarkably, plant DNA pol λ also possesses terminal transferase activity. In animal cells, this enzymatic activity has always been linked to the V(D)J recombination process during immunoglobulin gene rearrangement, but its presence in plant cells argues for a more fundamental and evolutionarily conserved function. Human DNA pol λ was suggested to have the highest similarity with the ancestor of the X-family DNA pols.10 It is a singlesubunit 68 kDa protein encoded by the POLL gene on the chromosome 10q23. DNA pol λ is composed of a N-terminal BRCT domain, a Ser-Pro rich region, and the C-terminal catalytic core. While the BRCT domain plays a role in mediating protein−protein interactions, the Ser-Pro rich region was shown to be a target for post-translational modifications.11 The 39 kDa catalytic core subunit of DNA pol λ is composed of an N-terminal 8 kDa domain and the polymerase domain. The X-ray crystal structure of the catalytic domain in complex with a DNA substrate containing a two nucleotide gap showed that DNA pol λ has two DNA binding sites, which, through exposure of the 3′ primer terminus, lead to DNA bending. Binding of the DNA downstream of the gap is predominantly mediated via the interaction of the 5′ terminus of the gap with the positively charged residues of the 8 kDa domain in the DNA pol λ and occurs during gap filling DNA synthesis associated with DNA repair The binding is enhanced by the presence of 5′ terminal phosphate, which at the same time stimulates the DNA pol λ polymerase activity (reviewed in ref 12; for more details, see sections 3 and 4).

2. BIOCHEMICAL FEATURES OF DNA POLYMERASE λ The catalytic core of DNA pol λ shows 32%−33% sequence identity to the corresponding region of the other human family X member DNA pol β.3 However, DNA pol λ presents some peculiar biochemical and catalytic properties. Despite its limited size and the lack of any auxiliary subunit, DNA pol λ possesses multiple catalytic activities: it can act as a template-dependent DNA pol, a terminal transferase, a dRPlyase, and a polynucleotide synthetase. The latter catalytic activity is unique to DNA pol λ, at least among human DNA pols, and enables this enzyme to synthesize polynucleotide chains starting from free nucleoside triphosphates, in the absence of any primer or template strand.13 Also the terminal transferase activity of DNA pol λ has different features from the similar activities of the family X members DNA pol μ and TdT. In fact, the activity of DNA pol λ prefers singlestranded DNA, and it is not active on 3′-recessed DNA ends such those in primer/template junctions. It is, at least in part, sequence specific and preferentially incorporates pyrimidine nucleotides.14 DNA pol λ prefers Mn2+ over Mg2+ as the metal activator, it efficiently synthesizes DNA from an RNA primer, and it can also incorporate rNTPs instead of dNTPs into a growing DNA 1937



Review

DNA pol λ in discriminating against 8-oxo-G:dAdo mismatches when bypassing this particular DNA damage (see also section 3).

Taken together, these results revealed a DNA pol λ-mediated oxidative stress response pathway that is important to sustain genome stability. Intriguingly, the very same pathway seems to be conserved also in plants.9 Many cellular DNA pols can incorporate beside dNTPs, also rNTPs during DNA synthesis. However, whether oxidative stress-triggered DNA repair synthesis contributes to genomic rNTPs incorporation was until very recently not fully understood. We showed that DNA pol β, to a greater extent than DNA pol λ and with different fidelity, can incorporate rNTPs opposite both undamaged bases as well as 8-oxo-G.33 Interestingly, and potentially relevant for future studies, the incorporation of rNTPs opposite 8-oxo-G delays initiation of the BER by DNA glycosylases, in particular MUTYH-mediated BER. Studies in DNA pols β- and λ-deficient cell extracts further suggested that DNA pol β levels can greatly affect incorporation of ribonucleotides opposite oxidative DNA lesions.33

3. DNA POLYMERASE λ IN BASE EXCISION REPAIR AND OXIDATIVE DAMAGE RESPONSE Exposure to the reactive oxygen species is one of the major sources of spontaneous damage. Reactive oxygen species damage essential cellular macromolecules including DNA. One of the most frequent oxidative DNA base lesions generated upon reactive oxygen species exposure is 8-oxo-G. The estimated steady-state level of 8-oxo-G lesions is about 103 per cell/per day in normal tissues and up to 105 per cell/per day in cancer tissues.21 The 8-oxo-G is particularly mutagenic in syn conformation as it functionally mimics dThd, thus resulting in efficient misincorporation of dAMP by replicative DNA pols.22 The dAdo(anti):8-oxo-G(syn) Hoogsteen mispair mimics normal base pair and is not detected by the 3′ → 5′ exonuclease proofreading activity of the replicative DNA pols. If not repaired, the dAdo:8-oxo-G mispair will be maintained in the genome and in the next round of replication give rise to G−C to T−A transversion mutations. The dAdo:8-oxo-G mispairs are substrates of MUTYH that specifically remove dAdo, thus leaving the 8-oxo-G lesion facing an abasic site in the DNA. For subsequent elimination of 8-oxo-G from the genome, it is essential to accurately incorporate dCMP opposite the lesion. By analyzing the 8-oxo-G bypass in the presence of purified human auxiliary factors PCNA, RP-A, and six different human DNA pols belonging to the B, Y, and X families, we showed that DNA pol λ has a unique specificity for incorporation of C opposite the lesion.23 This was further promoted by the presence of PCNA and RP-A resulting in 1200fold more efficient incorporation of accurate dC than the incorrect dA opposite the template 8-oxo-G by DNA pol λ, and 68-fold by DNA pol η.23 In addition to PCNA and RP-A, it was shown that the DNA polymerase δ-interacting protein 2 acts as a processivity factor for DNA pol λ during 8-oxo-G bypass.24 Besides the stimulatory effect, RP-A and PCNA act as molecular switches that repress DNA pol β activity and promote the DNA pol λ-mediated highly efficient and accurate 8-oxo-G bypass.25 Immunofluorescence experiments in cells exposed to oxidative stress linked MUTYH and DNA pol λ in the accurate base excision repair (BER) of dAdo:8-oxo-G mispairs.26 Use of whole cell extracts and subsequent in vitro reconstitution experiments indicated that this accurate repair pathway involves MUTYH, DNA pol λ, FEN1, and DNA ligase I and is thus characterized as long-patch BER. Very recently, the group of Garcia-Diaz provided additional structural insights into a potential mechanism of increased repair fidelity of MUTYH/DNA pol λmediated BER.27 They demonstrated that the discrimination against the pro-mutagenic syn-conformation occurs at the extension step and identified the Glu259 residue in DNA pol λ responsible for the selectivity (see also section 2). This residue acts as a kinetic switch since short-patch BER relies on the final ligation step on DNA ligase III, which is very inefficient in ligating the 3′ terminus of a 8-oxo-G:dCyt base pair.28 Thus, correct dCMP incorporation by the action of DNA pol λ shifts the repair choice toward long-patch BER, enhancing repair efficiency. Importance of DNA pol λ in response to oxidative stress has further been demonstrated at the cellular level, as DNA pol λ loss results in increased misincorporation of dAMP opposite 8-oxo-G as well as in hypersensitivity to oxidative stress.24 Indeed, DNA pol λ can also function as a backup enzyme for DNA pol β in BER,29−31 also thanks to its dRPlyase activity.32

4. DNA POLYMERASE λ IN NONHOMOLOGOUS END JOINING AND MICROHOMOLOGY MEDIATED END JOINING Double strand breaks (DSBs) are among the most dangerous DNA lesions, potentially leading to chromosomal instability and cell death if incorrectly resolved or left unrepaired. Two main pathways exist for the repair of DSBs in eukaryotic cells: homologous recombination (HR) and NHEJ. HR is active during the S phase, when the undamaged sister chromatid acts as a template for recombination. On the other hand, NHEJ acts throughout the cell cycle and is the main DSB repair pathway in higher organisms.34 DNA pol λ is involved in the gap-filling step of NHEJ. Through its BRCT domain, it can bind the XRCC4ligase IV complex, which is responsible for the final ligation step.35 DNA pol λ preferentially fills gaps when the broken ends have partially complementary overhangs.36 Biochemical evidence also suggests the involvement of DNA pol λ in an alternative Ku-independent and ligase IV-independent NHEJ pathway, which repairs broken DNA ends through a microhomology-mediated end joining (MMEJ) mechanism.37 This mechanism relies on regions of microhomology (five to 25 nucleotides) that anneal in the absence of Ku proteins to form a synaptic complex with gaps on both DNA strands. These gaps are subsequently filled by DNA pols and finally ligated by DNA ligase III or DNA ligase I.38 Using reconstituted in vitro MMEJ systems, it was shown that DNA pol λ can promote the formation of stable synapsis at microhomology regions, being able to fill the DNA gaps formed on both strands. This elongation step is stimulated by the 9−1−1 complex, which increases the processivity of DNA pol λ. Precise gap filling is ensured by the contact between the 8 kDa domain of DNA pol λ and the 5′phosphate of the terminal downstream nucleotide, which is facilitated by the “template scrunching” ability of DNA pol λ,18 which can thus process gaps even longer than 1 nt. Finally, DNA ligase I seals the nick,39 and this reaction is also stimulated by FEN1.40 5. REGULATION OF DNA POLYMERASE λ Our initial work suggested that cyclin-dependent kinase Cdk2 phosphorylates and interacts with human DNA pol λ.41 Indeed, the DNA pol λ phosphorylation pattern during cell cycle progression mimics the fluctuation of Cdk2/cyclin A activity. Experiments with phosphorylation-defective mutants suggested that Thr 553 is the main phosphorylation site, critical for 1938



Review

pol λ expression in the cancer tissue itself did not correlate with the smoking status of the patients.48 Further, a breast cancer study recently identified a cancer-related variant (R438W) of DNA pol λ. This variant exhibits lowered fidelity and impaired NHEJ efficiency. These properties correlated with an increased mutagenesis and chromosomal instability of cells expressing the mutant, further suggesting a role of this DNA pol λ variant in promoting carcinogenesis.49,50

maintenance of DNA pol λ stability. Unless phosphorylated at Thr 553, DNA pol λ is targeted for the proteasomal degradation via ubiquitination. DNA pol λ is in particular stabilized during cell cycle progression in late S and G2 phase, thus likely enabling DNA pol λ to properly conduct repair of damaged DNA during and after the S phase of the cell cycle.11 Further, experiments in different human cell lines showed that knockdown of DNA pol λ, but not of its close homologue DNA pol β, causes replication fork stress and activates the S-phase checkpoint, thus slowing S-phase progression.42 DNA pol λ thus also functions in rescuing stalled replication forks. Its absence becomes limiting for the cell survival when a functional checkpoint is missing, suggesting a synthesis sickness and lethality effect. These results seem to indicate that DNA pol λ is specifically required for normal cell cycle progression and it is functionally connected to the S-phase DNA damage response machinery.42 As just mentioned, DNA pol λ is phosphorylated by Cdk2/ CyclinA in late S and G2 phases of the cell cycle, promoting DNA pol λ stability by preventing it from being targeted for proteasomal degradation by ubiquitination.11,42 It, however, remained a mystery how the levels of DNA pol λ are controlled, how phosphorylation promotes its stability, and how is the engagement of DNA pol λ in active repair complexes coordinated. Analysis of E3 ubiquitin ligases revealed that HUWE1 as well as CHIP target DNA pol λ.43,44 It was further demonstrated that HUWE1 in particular mediates the DNA pol λ degradation and that the control of DNA pol λ levels by HUWE1 has functional consequences for the ability of mammalian cells to deal with 8-oxo-G lesions. Furthermore, phosphorylation of DNA pol λ by Cdk2/CyclinA counteracts HUWE1-mediated degradation by facilitating recruitment of DNA pol λ to chromatin into active 8-oxo-G repair complexes. This is achieved through an increase in DNA pol λ affinity for chromatin-bound MUTYH. Finally, DNA pol λ not engaged in active repair on chromatin is ubiquitinated and subjected to proteasomal degradation.44,45 Phosphorylation of DNA pol λ is also important for its role in NHEJ. It has been shown that DNA pol λ is phosphorylated by both the ATM and DNA-PK protein kinases on its Thr 204 residue and that this phosphorylation increases its interaction with the NHEJ multiprotein complex at the level of the broken DNA ends, thus facilitating the gap filling step.46

7. CONCLUSIONS In human cells, only four DNA pols (α, δ, ε, and γ) are required for the duplication of both nuclear and mitochondrial DNA. On the other hand, more than a dozen DNA pols are necessary to ensure the maintenance of the integrity of the genetic information. This is the result of the high degree of specialization of repair DNA pols, which possess special properties making them uniquely fit for either a particular DNA repair pathway or bypass of a particular DNA lesion. Despite their selectivity, a certain degree of redundancy exists among these enzymes, leading to potentially overlapping roles. In turn, this requires a careful regulation in terms of expression levels, intracellular localization, and timing of recruitment to a particular subcellular compartment. When such a tight regulation fails, these enzymes can be detrimental, rather than beneficial, to the cell, causing mutations and genetic instability. DNA pol λ is a typical example of such double-edged swords of the cell. This enzyme plays essential roles in many different repair pathways. Thus, while fundamentally beneficial to the cell, under some special circumstances, DNA pol λ can exert deleterious effects. For example, in the presence of unbalanced dNTP/rNTP pool ratios, DNA pol λ can incorporate rNTPs into DNA, even opposite DNA lesions. This, in turn, may delay BER, causing mutations and DNA instability. Finally, overexpression of DNA pol λ has been linked to tumorigenesis and may play a role in tumor chemoresistance to DNA damaging agents, thanks to the activation of MMEJ repair of DSBs. Understanding the molecular aspects of such dual role of DNA pol λ, particularly the mechanisms of its (de)regulation, might be exploited for the design of potential antitumoral targets. For example, suppression of DNA pol λ has been shown to induce synthetic lethality when combined with the protein kinase Chk1 inhibitors. Unfortunately, very few small molecule inhibitors of DNA pol λ have been described to date, both natural and synthetic, and even fewer of them seem selective and endowed with potent (i.e., nanomolar) inhibitory power. Thus, it is important to continue in the efforts for the identification of selective inhibitors targeting DNA pol λ, with the aim of improving our current arsenal of chemotherapeutic drugs active against tumor cells. In particular, inhibition of DNA repair mechanisms combined with traditional DNA damaging antitumoral agents may potentiate selective tumor killing. This, however, requires a better knowledge of how DNA repair mechanisms are altered in the tumor genetic background, particularly with respect to the regulation of specialized DNA repair pols.

6. DNA POLYMERASE λ AND CANCER An interesting study testing 68 different tumors measured the expression levels of a variety of DNA pols.47 Analysis of the two X family DNA pols β and λ, the two Y family DNA pols ι and κ, and the three replicative B family DNA pols α, δ, and ε indicated that in more than 45% of all analyzed tumors, at least one of the X or Y DNA pols was overexpressed. This was particularly pronounced for DNA pol β that was overexpressed in 30% of all tumors. DNA pols λ and ι were also overexpressed but less frequently than DNA pol β. All the 68 tumors were summarized in an overexpression scale that gave the following order: DNA pol β > DNA pol ι > DNA pol λ > DNA pol α > DNA pol δ > DNA pol κ > DNA pol ε. These data clearly indicated that the expression patterns of DNA pols in normal and cancer tissues are very complex, and the expression levels of the DNA pols are changed in tumors and can vary from one type of a tumor to another. In line with this observation, specific analysis of DNA pol λ levels in the lung epithelium of lung cancer patients showed that DNA pol λ expression in the bronchiolar epithelia is significantly correlated with the amount of habitual smoking. On the other hand, DNA

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AUTHOR INFORMATION

Corresponding Author

*E-mail: [email protected]. Phone: (+39) 0382546354. Fax: (+39) 0382422286. ORCID

Giovanni Maga: 0000-0001-8092-1552 1939



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Funding

The work in the authors’ laboratories has been partially supported by the Italian Association for Cancer Research AIRC (Grant No. IG15868 to G.M.), the Norwegian University of Science and Technology (NTNU) Onsager Fellowship to B.v.L., and the Research Council of Norway (Grant No. 263152/ F20 to B.v.L.).

Review

REFERENCES

(1) Hubscher, U., Spadari, S., Villani, G., and Maga, G. (2010) DNA Polymerases: Discovery, Characterization, and Functions in Cellular Transactions, World Scientific Publishing Co. Pte Ltd., Singapore. (2) van Loon, B., Woodgate, R., and Hubscher, U. (2015) DNA polymerases: Biology, diseases and biomedical applications. DNA Repair 29, 1−3. (3) Maga, G., Spadari, S., Villani, G., and Hubscher, U. (2017) Human DNA Polymerases: Biology, Medicine, and Biotechnology, World Scientific Publishing Co. Pte Ltd., Singapore. (4) Hubscher, U., and Maga, G. (2011) DNA replication and repair bypass machines. Curr. Opin. Chem. Biol. 15, 627−635. (5) Garcia-Diaz, M., Domínguez, O., López-Fernández, L. A., de Lera, L. T., Saníger, M. L., Ruiz, J. F., Párraga, M., García-Ortiz, M. J., Kirchhoff, T., del Mazo, J., Bernad, A., and Blanco, L. (2000) DNA polymerase lambda (Pol lambda), a novel eukaryotic DNA polymerase with a potential role in meiosis. J. Mol. Biol. 301, 851−867. (6) Uchiyama, Y., Kimura, S. T. Y., Yamamoto, T., Ishibashi, T., and Sakaguchi, K. (2004) Plant DNA polymerase lambda, a DNA repair enzyme that functions in plant meristematic and meiotic tissues. Eur. J. Biochem. 271, 2799−2807. (7) Uchiyama, Y., Takeuchi, R., Kodera, H., and Sakaguchi, K. (2009) Distribution and roles of X-family DNA polymerases in eukaryotes. Biochimie 91, 165−170. (8) Uchiyama, Y., Kimura, S., Yamamoto, T., Ishibashi, T., and Sakaguchi, K. (2004) Plant DNA polymerase lambda, a DNA repair enzyme that functions in plant meristematic and meiotic tissues. Eur. J. Biochem. 271, 2799−2807. (9) Amoroso, A., Concia, L., Maggio, C., Raynaud, C., Bergounioux, C., Crespan, E., Cella, R., and Maga, G. (2011) Oxidative DNA damage bypass in Arabidopsis thaliana requires DNA polymerase lambda and proliferating cell nuclear antigen 2. Plant Cell 23, 806−822. (10) Moon, A. F., Garcia-Diaz, M., Batra, V. K., Beard, W. A., Bebenek, K., Kunkel, T. A., Wilson, S. H., and Pedersen, L. C. (2007) The X family portrait: Structural insights into biological functions of X family polymerases. DNA Repair 6, 1709−1725. (11) Wimmer, U., Ferrari, E., Hunziker, P., and Hubscher, U. (2008) Control of DNA polymerase lambda stability by phosphorylation and ubiquitination during the cell cycle. EMBO Rep. 9, 1027−1033. (12) Garcia-Diaz, M., Bebenek, K., Gao, G., Pedersen, L. C., London, R. E., and Kunkel, T. A. (2005) Structure-function studies of DNA polymerase lambda. DNA Repair 4, 1358−1367. (13) Ramadan, K., Shevelev, I. V., Maga, G., and Hubscher, U. (2004) De novo DNA synthesis by human DNA polymerase lambda, DNA polymerase mu and terminal deoxyribonucleotidyl transferase. J. Mol. Biol. 339, 395−404. (14) Maga, G., Ramadan, K., Locatelli, G. A., Shevelev, I., Spadari, S., and Hübscher, U. (2005) DNA elongation by the human DNA polymerase lambda polymerase and terminal transferase activities are differentially coordinated by proliferating cell nuclear antigen and replication protein A. J. Biol. Chem. 280, 1971−1981. (15) Gosavi, R. A., Moon, A. F., Kunkel, T. A., Pedersen, L. C., and Bebenek, K. (2012) The catalytic cycle for ribonucleotide incorporation by human DNA Pol lambda. Nucleic Acids Res. 40, 7518−7527. (16) Garcia-Diaz, M., Bebenek, K., Krahn, J. M., Blanco, L., Kunkel, T. A., and Pedersen, L. C. (2004) A structural solution for the DNA polymerase lambda-dependent repair of DNA gaps with minimal homology. Mol. Cell 13, 561−572. (17) Garcia-Diaz, M., Bebenek, K., Krahn, J. M., Kunkel, T. A., and Pedersen, L. C. (2005) A closed conformation for the Pol lambda catalytic cycle. Nat. Struct. Mol. Biol. 12, 97−98. (18) Martin, M. J., Garcia-Ortiz, M. V., Gomez-Bedoya, A., Esteban, V., Guerra, S., and Blanco, L. (2013) A specific N-terminal extension of the 8 kDa domain is required for DNA end-bridging by human Polmu and Pollambda. Nucleic Acids Res. 41, 9105−9116. (19) Picher, A. J., García-Díaz, M., Bebenek, K., Pedersen, L. C., Kunkel, T. A., and Blanco, L. (2006) Promiscuous mismatch extension by human DNA polymerase lambda. Nucleic Acids Res. 34, 3259−3266.

Notes

The authors declare no competing financial interest. Biographies Barbara van Loon obtained her PhD at the University of Zurich (Zurich, Switzerland) under supervision of Prof. U. Hübscher. Upon graduation, Barbara moved to the Massachusetts Institute of Technology (Cambridge, MA, USA) and joined as a Postdoctoral Fellow group of Prof. L.D. Samson. She then returned to the University of Zurich started her independent career. In 2016, Barbara moved to Norwegian University of Science and Technology (Trondheim, Norway) where she is currently associate professor. Barbara’s major contribution to the field of DNA repair includes unraveling role of DNA polymerases in the oxidative stress response as well as discovering novel roles and functions of DNA glycosylases in response to alkylation damage. Ulrich Hü b scher graduated in Veterinary Medicine and did postgraduate studies in Biochemistry and Molecular Biology in Switzerland. After postdoc years in the laboratories of Arthur Kornberg (Stanford) and Robin Holliday (Mill Hill), he started his own work in 1981 in Zurich, where he became Professor in 1989. He devoted his research since then to functions of DNA polymerases. In over 300 publications, he contributed to different biological functions of different DNA polymerases from prokaryotes and eukaryotes and their auxiliary proteins (replication protein A, replication factor C, and proliferating cell nuclear antigen). He is a member of the Swiss Academy of Medical Sciences. Giovanni Maga graduated in Biology from the University of Pavia (Italy) and was a postdoc in the laboratory of Ulrich Hübscher (University of Zürich). Since 2006, he is Head of the DNA Enzymology & Molecular Virology Unit at the Institute of Molecular Genetics IGMCNR in Pavia. In more than 230 publications, he investigated the enzymatic systems responsible for the duplication and repair of the genetic information in human cells and viruses, aiming both at the elucidation of the basic molecular processes and at the exploitation of novel enzymatic targets for antiviral and anticancer chemotherapy.

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ABBREVIATIONS 8-oxo-G, 7,8-dihydro-8-oxoguanine; AEP, archaeo-eukaryotic primases; BER, base excision repair; BRCT, breast-cancersusceptibility protein-1 C-terminal-like; CHIP, carboxy terminus of Hsp70-interacting protein; DNA pol, DNA polymerase; dNTPs, deoxynucleosides triphosphates; dRPlyase, 5′-2-deoxyribose-5-phosphate lyase; DSBR, double strand break repair; DSBs, double strand breaks; FEN1, flap endonuclease 1; HR, homologous recombination; HUWE1, HECT UBA and WWE domain-containing protein 1; MMEJ, microhomology-mediated end joining; MUTYH, MutY DNA glycosylase homologue; NHEJ, nonhomologous end joining; PCNA, proliferating cell nuclear antigen; rNTPs, ribonucleosides triphosphates; RP-A, replication protein A; RT, reverse transcriptase; TdT, terminal deoxynucleotidyl transferase; TLS, translesion DNA synthesis; XRCC4, X-ray repair cross-complementing protein 4 1940



Review

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Living on the Edge: DNA Polymerase Lambda between Genome

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