Mutation Research/Genetic Toxicology and Environmental Mutagenesis
MinireviewFilling gaps in translesion DNA synthesis in human cells
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.
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2024, Journal of BiotechnologyThe accurate bypass of pyrimidine dimers by DNA polymerase eta contributes to ultraviolet-induced mutagenesis
2024, Mutation Research - Fundamental and Molecular Mechanisms of MutagenesisCurrent state of knowledge of human DNA polymerase eta protein structure and disease-causing mutations
2022, Mutation Research - Reviews in Mutation ResearchCitation 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 RepairCitation 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 RepairCitation 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 CellCitation 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).
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Both authors contributed equally to this work.