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How to Fix DNA-Protein Crosslinks

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How to Fix DNA-Protein Crosslinks How to fix DNA-protein crosslinks Kühbacher, Ulrike; Duxin, Julien P Published in: DNA Repair DOI: 10.1016/j.dnarep.2020.102924 Publication date: 2020 Document version Publisher's PDF, also known as Version of record Document license: CC BY-NC-ND Citation for published version (APA): Kühbacher, U., & Duxin, J. P. (2020). How to fix DNA-protein crosslinks. DNA Repair, 94, [102924]. https://doi.org/10.1016/j.dnarep.2020.102924 Download date: 05. okt.. 2021 DNA Repair 94 (2020) 102924 Contents lists available at ScienceDirect DNA Repair journal homepage: www.elsevier.com/locate/dnarepair How to fix DNA-protein crosslinks T Ulrike Kühbacher, Julien P. Duxin* The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark ARTICLE INFO ABSTRACT Keywords: Proteins that act on DNA, or are in close proximity to it, can become inadvertently crosslinked to DNA and form DNA-protein crosslinks (DPCs) highly toxic lesions, known as DNA-protein crosslinks (DPCs). DPCs are generated by different chemother- DNA replication apeutics, environmental or endogenous sources of crosslinking agents, or by lesions on DNA that stall the cat- DNA repair alytic cycle of certain DNA processing enzymes. These bulky adducts impair processes on DNA such as DNA replication or transcription, and therefore pose a serious threat to genome integrity. The large diversity of DPCs suggests that there is more than one canonical mechanism to repair them. Indeed, many different enzymes have been shown to act on DPCs by either processing the protein, the DNA or the crosslink itself. In addition, the cell cycle stage or cell type are likely to dictate pathway choice. In recent years, a detailed understanding of DPC repair during S phase has started to emerge. Here, we review the current knowledge on the mechanisms of replication-coupled DPC repair, and describe and also speculate on possible pathways that remove DPCs outside of S phase. Moreover, we highlight a recent paradigm shifting finding that indicates that DPCs are not always detrimental, but can also play a protective role, preserving the genome from more deleterious forms of DNA damage. 1. DNA-protein crosslinks: a diverse class of lesions 1.1.1. Endogenous crosslinking agents An important endogenous source of crosslinking agents is alde- In contrast to other types of DNA lesions, DPCs are highly hetero- hydes. Reactive aldehydes, such as formaldehyde, are found at high geneous and differ from one another depending on the nature ofthe concentration in human plasma [3]. Formaldehyde is generated as a protein adducted to DNA, the chemistry of the crosslink and the DNA byproduct of different metabolic processes such as histone demethyla- surrounding the adduct. Thus, a thorough classification of DPCs is tion or lipid peroxidation [4–6]. Formaldehyde treatment is often used challenging since each of the three components forming a DPC is likely as a proxy of DPC sensitivity in cells. This is because formaldehyde to contribute to the mechanism of repair. Here, we present a simple crosslinks proteins to DNA via a methylene bridge that involves the classification based on the DNA component of the crosslink, which can exocyclic amine of DNA bases and different protein amino acids greatly impact the faith of the replisome encountering the lesion (e.g. (mainly lysine, cysteine, histidine or tryptophan) (Fig. 1A, i) [7], al- by inducing replisome stalling or replication fork collapse), and the way though a recent study suggests a two carbon atoms linkage instead [8]. the DPC is sensed and repaired. Acetaldehyde, a byproduct of ethanol metabolism [9], is also able to crosslink proteins to DNA. Acetaldehyde can form different types of 1.1. DPCs on double-stranded DNA DNA adducts with 1,N2-propano-2′-deoxyguanosine (PdG) being the most toxic one. The subsequent formation of DPCs involves the ring- Proteins crosslink to uninterrupted double-stranded DNA (dsDNA) opened isomer of PdG, containing a free aldehyde group that most by the action of different crosslinking agents, including chemother- likely forms a Schiff base-mediated crosslink with a basic amino acid apeutics, reactive aldehydes, ultraviolet (UV) light, ionizing radiation such as arginine or lysine [10,11]. Other reactive aldehydes present in (IR) and different transition metals [1,2]. DPCs induced by crosslinking cells, such as malondialdehyde and acrolein, have also been shown to agents can, in theory, link any protein in close proximity to DNA. Thus, crosslink DNA and proteins together [12,13]. Importantly, reactive al- these DPCs are highly diverse and exhibit different sizes and chemis- dehydes are known to generate a wide spectrum of other lesions (e.g. tries. protein-protein crosslinks, DNA adducts, and DNA interstrand cross- links (ICLs)) [14]. In the case of formaldehyde, it likely favors protein- ⁎ Corresponding author. E-mail address: [email protected] (J.P. Duxin). https://doi.org/10.1016/j.dnarep.2020.102924 Received 7 May 2020; Received in revised form 3 July 2020; Accepted 5 July 2020 Available online 09 July 2020 1568-7864/ © 2020 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). U. Kühbacher and J.P. Duxin DNA Repair 94 (2020) 102924 Fig. 1. DPC classification based on the DNA component of the crosslink. (A) Illustration of DPCs on dsDNA. (B) Illustration of a specific DPC that crosslinks to AP sites on ssDNA. (C) and (D) illustrate specific DPCs flanked byaSSBor DSB, respectively. protein linkages over protein-DNA linkages because DPC formation by and proteins, mainly involving the N7 position of guanine and cysteine formaldehyde requires the prior disruption of Watson-Crick base amino side chains [19]. Studies indicate that cells deficient in DPC pairing to expose DNA’s exocyclic amines [15]. Thus, it is often unclear removal (e.g. SPRTN-deficient cells) are sensitive to cisplatin treatment, how these crosslinking agents induce cellular toxicity, and caution suggesting that DPCs contribute to the cytotoxic effects of some of these should be taken when assuming that the cytotoxic effect of for- chemotherapeutics [20,21]. However, it is currently unknown how maldehyde is mainly driven by DPCs. large the fraction of DPCs generated by cisplatin derivatives is in cancer patients, and a big challenge is to understand whether DPC generation and/or repair contribute to the therapeutic effects and/or tumor re- 1.1.2. Chemotherapeutics sistance development. Although chemotherapeutics, such as cisplatin derivatives and ni- Another drug, 5′-aza-2-deoxycytidine (5-aza-dC), commonly used in trogen mustards, are mainly known to form DNA adducts and DNA the treatment of myelodysplastic syndromes, generates DPCs by trap- ICLs, they can also form DPCs [16]. Cisplatin can induce DPCs by at- ping the DNA (cytosine-5)-methyltransferase 1 (DNMT1) on its re- tacking the N7 atom of purine bases, which can then be connected to cognition site. DNMT1 maintains the methylation pattern on DNA fol- cysteine, arginine, and lysine side chains by a subsequent nucleophilic lowing DNA replication. It recognizes hemi-methylated DNA and attack on the platinum center (Fig. 1A, ii) [17]. Nitrogen mustards, transfers methyl groups to the newly synthesized strand [22]. In- which are one of the oldest classes of chemotherapeutics [18], can also corporation of the cytosine analog 5-aza-dC during replication causes generate DPCs via sequential alkylation of nucleophilic sites in DNA 2 U. Kühbacher and J.P. Duxin DNA Repair 94 (2020) 102924 trapping of DNMT1 behind the replication fork. When DNMT1 me- is typically generated when proteins that act on DNA become covalently thylates the daughter strand, the lack of a proton at the N5 position of crosslinked to DNA in an intermediate step of their catalytic cycle. The the triazine ring disables DNMT1 release by β-elimination and results in most prominent example are topoisomerases. the permanent trapping of DNMT1 (Fig. 1A, iii) [23,24]. This causes global hypomethylation in cells, which leads to re-expression of tumor 1.3.1. TOP1 cleavage complexes (TOP1ccs) suppressor genes [25,26]. The therapeutic effect of 5-aza-dC treatment Topoisomerase 1 (TOP1) acts on DNA to release torsional stress likely originates from DNA hypomethylation [27], but whether during replication or transcription [42]. To do so, its catalytic tyrosine DNMT1-DPCs also contribute to this effect remains unclear. In analogy attacks the sugar phosphate backbone of DNA, introducing a SSB con- with 5-aza-dC, 5-fluoro-2-deoxycytosine also traps cytosine DNA me- fined by a phosphotyrosyl linkage. The free DNA strand can thenrotate thyltransferases, and this method can be used to model DPCs on dsDNA to release torsional stress. Finally, the DNA 5′ OH attacks the phos- [28,29]. photyrosine linkage and the nick is religated, releasing the covalent protein adduct. However, neighboring DNA lesions or intercalating 1.1.3. Other exogenous sources of crosslinking agents agents (such as camptothecin or topotecan) can displace the 5′ OH, UV and IR cause a spectrum of different lesions on DNA, such as inhibiting religation of the nick and trapping the enzyme at the 3′ end base damage, single-strand breaks (SSBs), double-strand breaks (DSBs) of DNA (Fig. 1C, i) [43]. Because TOP1 lesions are particularly detri- and DPCs. Interestingly, the proportional distribution of these lesions mental to highly proliferative cells, TOP1 poisons are widely used in the generated by UV or IR is dependent on the oxygen levels in the cellular clinic to treat ovarian, cervical and lung cancers. The TOP1 covalent environment [30]. Under hypoxic conditions, as can be found in solid intermediate is called TOP1 cleavage complex (TOP1cc) and requires tumors, DPCs are thought to be the main lesion caused by these agents, tyrosyl-DNA phosphodiesterase 1 (TDP1) to reverse the crosslink [44].
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