Minireview
Filling gaps in translesion DNA synthesis in human cells

https://doi.org/10.1016/j.mrgentox.2018.02.004Get rights and content

Highlights

  • TLS polymerases replicate DNA damage at the fork and at gaps behind the fork.

  • The nature of the lesion and TLS polymerases available define how TLS occurs.

  • TLS polymerases act on non-canonical DNA structures and DNA repair mechanisms.

  • Induction of TLS polymerases in human cells resembles the SOS response in bacteria.

Abstract

During DNA replication, forks may encounter unrepaired lesions that hamper DNA synthesis. Cells have universal strategies to promote damage bypass allowing cells to survive. DNA damage tolerance can be performed upon template switch or by specialized DNA polymerases, known as translesion (TLS) polymerases. Human cells count on more than eleven TLS polymerases and this work reviews the functions of some of these enzymes: Rev1, Pol η, Pol ι, Pol κ, Pol θ and Pol ζ. The mechanisms of damage bypass vary according to the lesion, as well as to the TLS polymerases available, and may occur directly at the fork during replication. Alternatively, the lesion may be skipped, leaving a single-stranded DNA gap that will be replicated later. Details of the participation of these enzymes are revised for the replication of damaged template. TLS polymerases also have functions in other cellular processes. These include involvement in somatic hypermutation in immunoglobulin genes, direct participation in recombination and repair processes, and contributing to replicating noncanonical DNA structures. The importance of DNA damage replication to cell survival is supported by recent discoveries that certain genes encoding TLS polymerases are induced in response to DNA damaging agents, protecting cells from a subsequent challenge to DNA replication. We retrace the findings on these genotoxic (adaptive) responses of human cells and show the common aspects with the SOS responses in bacteria. Paradoxically, although TLS of DNA damage is normally an error prone mechanism, in general it protects from carcinogenesis, as evidenced by increased tumorigenesis in xeroderma pigmentosum variant patients, who are deficient in Pol η. As these TLS polymerases also promote cell survival, they constitute an important mechanism by which cancer cells acquire resistance to genotoxic chemotherapy. Therefore, the TLS polymerases are new potential targets for improving therapy against tumors.

Introduction

Genome stability is fundamental for life, and evolution has equipped the cells with many different ways to cope with DNA damage, which occur either spontaneously, due to the intrinsic chemical properties of DNA, endogenously by metabolite reactive products, or after exposure to physical or chemical agents from the environment. Thus, different excision repair pathways can remove structural base alterations from the DNA molecule, directing the recovery of the original double helix structure. However, these mechanisms are not always completely effective, or simply may not occur before basic DNA processes such as replication or transcription face the damaged templates. In fact, DNA synthesis may be blocked by unrepaired DNA lesions, which can lead to cell death [1,2]. A clever way to avoid such problems is simply sense DNA damage and signal for the cells to stop cell cycle before DNA synthesis or mitosis starts, processes known as cell cycle checkpoints [3]. Still, when DNA damage are not removed and DNA synthesis confronts such obstacles, the cells have mechanisms to signal for repair or allow the DNA to proceed despite of the lesion, helping the cells to tolerate the damage.

The relevance of these processes to the protection of organisms is dramatically evidenced by patients with human disorders, who carry mutations that affect directly the mechanisms involved in dealing with damaged DNA. Several clinical phenotypes are often associated with these disorders, but the most commonly observed are increased carcinogenesis and symptoms normally associated with premature aging, including neurological problems and neurodegeneration. Examples of such diseases are the syndromes xeroderma pigmentosum (XP), ataxia telangiectasia (AT) and Fanconi anemia (FA). The three are involved in different processes of DNA damage and present high frequency of cancer, but may also present neurodegeneration phenotypes [[4], [5], [6], [7]]

As the focus of this review is DNA synthesis of damaged templates, the example of XP will be detailed. The most prominent symptoms of XP patients affect the skin, where many lesions, including tumors, are frequently observed, but only in regions exposed to the sunlight. Unfortunately, the face is often one of these regions, with severe complications to these patients. XP skin become dry and highly pigmented, and also may develop precancerous lesions, such as actinic keratosis, and tumors (non melanoma and melanoma). Most of the XP patients are defective in the removal of DNA damage, including lesions induced by UV, a process known as Nucleotide Excision Repair (NER). However, some XP patients, who in general have a milder clinical phenotype, were discovered to have normal capacity to remove UV-induced DNA lesions, but their cells failed to replicate efficiently the unrepaired damage [8]. These patients were named XP variants (XP-V). Almost twenty-five years later, the inability of XP-V cells to replicate damaged DNA was demonstrated to be due to a defect on a DNA polymerase responsible for lesions bypass, DNA polymerase eta (Pol eta or Pol η), now known as a translesion synthesis (TLS) DNA polymerase [[9], [10], [11]]. Since this breakthrough, several progresses were made in the understanding of how cells manage to replicate DNA lesions. The need of such mechanisms for cells to cope with DNA damage was revealed by the identification of many other TLS polymerases in human cells. However, their functions are not fully understood yet, leading to many gaps in our knowledge. These gaps are slowly being filled with the discovery of the molecular mechanisms involved in the replication of damaged DNA templates. This review will give an overview of what is known about these TLS polymerases and the strategies known of how they help cells to survive insults, although, in general, at the expense of generating mutations. As the initial experiments were performed with UV-irradiation, most of what is known about these TLS polymerases is related to UV-induced lesions, as detailed below. However, one must bear in mind that other types of DNA damage are also subject to these tolerance mechanisms, and thus the reach of such knowledge may have important impact on cells ability to survive genotoxic agents, including tumor cells resistance to chemotherapeutic agents.

Section snippets

UVC-induced DNA damage: a model to study DNA damage tolerance

The UV components of sunlight that reaches the Earth surface are one of the most carcinogenic agents humans are exposed to, and the leading cause of skin cancer [4,12]. UV light causes different types of DNA damage through indirect and direct modes. UV rays can be absorbed by chromophores present in skin cells, leading to the generation of reactive species of oxygen (ROS) that can damage the DNA by oxidizing bases [13]. UV light can also be directly absorbed by the DNA molecule, leading to the

DNA damage tolerance by translesion DNA synthesis (TLS) polymerases

In human cells, 6-4PPs are completely removed within 3–6 h after exposure to UV radiation, while about 50% of CPDs still persist 24 h later [[20], [21], [22]]. An important outcome of this is that most cells progressing though the S phase (DNA synthesis) of the cell cycle will encounter CPD lesions before their complete removal. Strikingly, cells from XP patients, defective in NER, progressing through the S-phase will have to deal with both CPDs and 6-4PPs.

Bulky lesions on DNA physically block

Roles of TLS polymerases outside DNA damage tolerance

Besides their role in the replication of damaged DNA, TLS polymerases are also responsible for the replication of non-canonical DNA structures that interfere with the normal process of DNA replication. They also function in several other DNA metabolism processes, including excision and recombination DNA repair mechanisms and the development of the immune response, while generating mutations during the somatic hypermutation (SHM) process.

Help! SOS response in bacteria

Initial studies in bacteria indicated the existence of an intricate regulation mechanism, where DNA repair systems are induced after a genotoxic stress, in a way to save the cells, although at the price of mutations in the progeny. Prior exposure of cells to low doses of UV is capable of greatly increasing the survival of UV-irradiated viral particles, a phenomenon called the Weigle reactivation [202]. Later, it was shown that the induction of the so-called SOS responses in bacteria is

Conclusions and perspectives

Although known for many decades, the relevance of TLS in genome stability is normally considered secondary to mechanisms that effectively remove DNA damage. However, the existence of so many TLS polymerases, with the intricate mechanisms that guarantee damage tolerance, challenges this notion. As an important paradox, though naturally error-prone, these proteins provide us strong protection against mutagenesis, and cancer, as exemplified by the high incidence of tumors in XP-V patients. Most of

Acknowledgments

This work was supported by FAPESP, São Paulo, Brazil, (Grants # 2014/15982-6 and 2013/21075-9); CNPq and CAPES (Brasília, DF, Brazil). We thank Dr. Julian Sale (Medical Research Council Laboratory of Molecular Biology, Cambridge, UK) for critical reading of this review.

References (247)

  • G.L. Moldovan et al.

    PCNA, the maestro of the replication fork

    Cell

    (2007)
  • P.L. Kannouche et al.

    Interaction of human DNA polymerase eta with monoubiquitinated PCNA: A possible mechanism for the polymerase switch in response to DNA damage

    Mol. Cell

    (2004)
  • R. Kanao et al.

    Regulation of DNA damage tolerance in mammalian cells by post-translational modifications of PCNA

    Mutat. Res. Mol. Mech. Mutagen.

    (2017)
  • H.D. Ulrich

    Regulating post-translational modifications of the eukaryotic replication clamp PCNA

    DNA Repair (Amst.)

    (2009)
  • Q. Gueranger et al.

    Role of DNA polymerases eta, iota and zeta in UV resistance and UV-induced mutagenesis in a human cell line

    DNA Repair (Amst.)

    (2008)
  • R.E. Johnson et al.

    Fidelity of human DNA polymerase ɳ

    J. Biol. Chem.

    (2000)
  • P. Temviriyanukul et al.

    Temporally distinct translesion synthesis pathways for ultraviolet light-induced photoproducts in the mammalian genome

    DNA Repair (Amst.)

    (2012)
  • J.-Y. Choi et al.

    Translesion synthesis across abasic lesions by human B-family and Y-family DNA polymerases α, δ, η, ι, κ, and REV1

    J. Mol. Biol.

    (2010)
  • A.-L. Ross et al.

    The catalytic activity of REV1 is employed during immunoglobulin gene diversification in DT40

    Mol. Immunol.

    (2006)
  • J.G. Jansen et al.

    Roles of mutagenic translesion synthesis in mammalian genome stability, health and disease

    DNA Repair (Amst)

    (2015)
  • C.E. Edmunds et al.

    PCNA ubiquitination and REV1 define temporally distinct mechanisms for controlling translesion synthesis in the avian cell line DT40

    Mol. Cell

    (2008)
  • A.E. Vidal et al.

    Proliferating cell nuclear antigen-dependent coordination of the biological functions of human DNA polymerase

    J. Biol. Chem.

    (2004)
  • A. Vaisman et al.

    Sequence context-dependent replication of DNA templates containing UV-induced lesions by human DNA polymerase ι

    DNA Repair (Amst).

    (2003)
  • R.P. Barnes et al.

    DNA polymerases eta and kappa exchange with the polymerase delta holoenzyme to complete common fragile site synthesis

    DNA Repair (Amst)

    (2017)
  • M. Seki et al.

    DNA polymerase theta (POLQ) can extend from mismatches and from bases opposite a (6-4) photoproduct

    DNA Repair (Amst)

    (2008)
  • N. Rhind et al.

    Signaling pathways that regulate cell division

    Cold Spring Harb. Perspect. Biol.

    (2012)
  • C.F.M. Menck et al.

    DNA repair diseases: what do they tell us about cancer and aging?

    Genet. Mol. Biol.

    (2014)
  • C. Rothblum-Oviatt et al.

    Ataxia telangiectasia: a review

    Orphanet J. Rare Dis.

    (2016)
  • A. Gueiderikh et al.

    A never-ending story: the steadily growing family of the FA and FA-like genes

    Genet. Mol. Biol.

    (2017)
  • A.R. Lehmann et al.

    Xeroderma pigmentosum cells with normal levels of excision repair have a defect in DNA synthesis after UV-irradiation

    Proc. Natl. Acad. Sci. U. S. A.

    (1975)
  • C. Masutani et al.

    The XPV (xeroderma pigmentosum variant) gene encodes human DNA polymerase eta

    Nature

    (1999)
  • R.E. Johnson

    hRAD30 mutations in the variant form of xeroderma pigmentosum

    Science

    (1999)
  • A. Vaisman et al.

    Translesion DNA polymerases in eukaryotes: what makes them tick?

    Crit. Rev. Biochem. Mol. Biol.

    (2017)
  • G.P. Pfeifer

    Formation and processing of UV photoproducts: effects of DNA sequence and chromatin environment

    Photochem. Photobiol.

    (1997)
  • A.P. Schuch et al.

    DNA damage as a biological sensor for environmental sunlight

    Photochem. Photobiol. Sci.

    (2013)
  • A.P. Schuch et al.

    Development of a DNA-dosimeter system for monitoring the effects of solar-ultraviolet radiation

    Photochem. Photobiol. Sci.

    (2009)
  • R.P. Rastogi et al.

    Molecular mechanisms of ultraviolet radiation-induced DNA damage and repair

    J. Nucleic Acids

    (2010)
  • L. Riou et al.

    The relative expression of mutated XPB genes results in xeroderma pigmentosum/Cockayne’s syndrome or trichothiodystrophy cellular phenotypes

    Hum. Mol. Genet.

    (1999)
  • J. Hu et al.

    Genome-wide analysis of human global and transcription-coupled excision repair of UV damage at single-nucleotide resolution

    Genes Dev.

    (2015)
  • M. Matsumoto et al.

    Perturbed gap-filling synthesis in nucleotide excision repair causes histone H2AX phosphorylation in human quiescent cells

    J. Cell Sci.

    (2007)
  • M.K. Zeman et al.

    Causes and consequences of replication stress

    Nat. Cell Biol.

    (2013)
  • M. Berti et al.

    Replication stress: getting back on track

    Nat. Struct. Mol. Biol.

    (2016)
  • T.S. Byun et al.

    Functional uncoupling of MCM helicase and DNA polymerase activities activates the ATR-dependent checkpoint

    Genes Dev.

    (2005)
  • K.A. Cimprich et al.

    ATR: an essential regulator of genome integrity

    Nat. Rev. Mol. Cell Biol.

    (2008)
  • J.C. Saldivar et al.

    The essential kinase ATR: ensuring faithful duplication of a challenging genome

    Nat. Rev. Mol. Cell Biol.

    (2017)
  • J.E. Sale

    Competition, collaboration and coordination – determining how cells bypass DNA damage

    J. Cell Sci.

    (2012)
  • F. Prado

    Homologous recombination maintenance of genome integrity during DNA damage tolerance

    Mol. Cell. Oncol.

    (2014)
  • C.F.M. Menck et al.

    Resistance of 3T3 mouse cells to UV light in relation to excision and transfer ofdimers to daughter strands

    Photochem. Photobiol.

    (1982)
  • A.R. Chaudhuri et al.

    Replication fork stability confers chemoresistance in BRCA-deficient cells

    Nature

    (2016)
  • R. Zellweger et al.

    Rad51-mediated replication fork reversal is a global response to genotoxic treatments in human cells

    J. Cell Biol.

    (2015)
  • Cited by (26)

    • The accurate bypass of pyrimidine dimers by DNA polymerase eta contributes to ultraviolet-induced mutagenesis

      2024, Mutation Research - Fundamental and Molecular Mechanisms of Mutagenesis
    • Current state of knowledge of human DNA polymerase eta protein structure and disease-causing mutations

      2022, Mutation Research - Reviews in Mutation Research
      Citation Excerpt :

      The human genome encodes sixteen DNA polymerases, and at least six of these enzymes replicate damaged DNA templates. Four of these belong to the Y family, which includes POLη, POLι, POLκ, and REV1 DNA Directed Polymerase (REV1), and the other two are POLζ (REV3 L, of the B family) and PrimPol (AEP-family) [19]. POLη is the most studied and well-known TLS polymerases and the only polymerase linked to a human syndrome (XP-V).

    • Daughter-strand gaps in DNA replication – substrates of lesion processing and initiators of distress signalling

      2021, DNA Repair
      Citation Excerpt :

      Finally, the discovery of an entire class of DNA polymerases revealed another pathway of DNA damage bypass now known as translesion synthesis (TLS) (Fig. 2E). TLS polymerases are highly conserved between bacteria and eukaryotes and most organisms harbour several enzymes specialised on different types of lesions [55–57]. They mostly belong to the so-called Y-family of DNA polymerases and harbour shallow active sites that tolerate non-native templates, thus allowing the enzymes to polymerise across lesions with reduced processivity and fidelity.

    • Error-prone bypass patch by a low-fidelity variant of DNA polymerase zeta in human cells

      2021, DNA Repair
      Citation Excerpt :

      It is possible that two specialized Pols participate in TLS where one Pol inserts correct or incorrect dNMPs opposite a lesion and another Pol extends the primer from the lesion [11,12]. TLS may occur at the advancing replication fork or behind the fork as a post-replication gap-filling DNA synthesis [6,7,13]. Typical examples of specialized Pols are Pol η, Pol ι, Pol κ and REV1, which are the Y-family Pols, and Pol ζ, a B-family enzyme [14–16].

    • To skip or not to skip: choosing repriming to tolerate DNA damage

      2021, Molecular Cell
      Citation Excerpt :

      6-4PPs cause a more pronounced distortion of the DNA double helix compared with CPDs. Although CPDs are efficiently bypassed by the TLS polymerase POL η at the replication fork, formation of 6-4PPs leads to ssDNA gap accumulation behind replication forks in DNA repair-deficient mouse embryonic and human fibroblasts, suggesting that tolerance of UV-induced 6-4PPs involves replication fork repriming (Jansen et al., 2009; Quinet et al., 2018). In agreement with the proposed role of repriming in the bypass of bulky 6-4PPs, PRIMPOL binding to chromatin increases after treatment with UV-C, and PRIMPOL depletion, or loss of its primase activity, impairs replication fork restart upon UV-C irradiation (Mourón et al., 2013).

    View all citing articles on Scopus
    1

    Both authors contributed equally to this work.

    View full text