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International audience; Exposure to solar UV is at the origin of numerous photodegradation pathways in biomolecules. Tryptophan is readily modified by UVB radiation into ring-opened and oxidized photoproducts. One of them, 6-formylindolo[3,2-b]carbazole (FICZ), has been extensively studied in the recent years because it very efficiently binds to AhR, a major factor in numerous biological processes, such as metabolism of xenobiotics. Unfortunately, little information is available on the actual yield of FICZ upon exposure to low and biologically relevant doses of UV radiation. In the present work, we used a sensitive and specific HPLC-tandem mass spectrometry assay to quantify a series of photoproducts induced by UVB and simulated sunlight (SSL) in solutions of tryptophan. FICZ represented only a minute amount of the photoproducts (0.02% and 0.03%, respectively). Experiments were repeated in culture medium where the yield of FICZ was also found to be very low, even when Trp was added. Last, no FICZ could be detected in cytosolic fractions of cultured cells exposed to SSL. Altogether, the present results show that FICZ is a very minor photoproduct and that it cannot be considered as the only endogenous photoproduct responsible for the induction of AhR-dependent responses in UV-irradiated cells. This article is protected by copyright. All rights reserved.

International audience; Sulfur is present in several nucleosides within tRNAs. In particular, thiolation of the universally conserved methyl-uridine at position 54 stabilizes tRNAs from thermophilic bacteria and hyperthermo-philic archaea and is required for growth at high temperature. The simple nonredox substitution of the C2-uridine carbonyl oxygen by sulfur is catalyzed by tRNA thiouridine synthetases called TtuA. Spectroscopic, enzymatic, and structural studies indicate that TtuA carries a catalytically essential [4Fe-4S] cluster and requires ATP for activity. A series of crystal structures shows that (i) the cluster is ligated by only three cysteines that are fully conserved, allowing the fourth unique iron to bind a small ligand, such as exogenous sulfide, and (ii) the ATP binding site, localized thanks to a protein-bound AMP molecule, a reaction product, is adjacent to the cluster. A mechanism for tRNA sulfuration is suggested, in which the unique iron of the catalytic cluster serves to bind exogenous sul-fide, thus acting as a sulfur carrier. tRNA modification | thiolation | [Fe-S] cluster | thiouridine synthetase | U54-tRNA T he cellular translation machinery contains essential components such as tRNAs. To achieve their function, they feature a great variety of well-conserved posttranscriptional chemical modifications. Sulfur is present in several of these modified nucleosides: thiouridine and derivatives (s 4 U8, s 2 U34, and m 5 s 2 U54), 2-thioadenosine derivatives (ms 2 i 6 A37 and ms 2 t 6 A37), and 2-thiocytidine (s 2 C32). However, mechanisms of sulfur insertion into tRNAs are largely unknown, and the enzymes responsible for these reactions are incompletely characterized. Whereas redox conversion of a C-H to a C-S bond (synthesis of ms 2 i 6 A37 and ms 2 t 6 A37) depends on redox enzymes from the RadicalS -adenosyl-L-methionine iron-sulfur enzyme family, simple nonredox conversion of C = O to C = S group (synthesis of s 2 U34 and s 4 U8) is not expected to require such redox clusters. Intriguingly, we recently discovered that the ATP-dependent formation of s 2 C32 in some tRNAs is catalyzed by an iron-sulfur enzyme, TtcA (1). However, the role of its cluster has not been defined. In the same superfamily, TtuA enzymes catalyze the C2-thiolation of uridine 54 in the T loop of thermophilic tRNAs (Fig. 1A), allowing stabilization of tRNAs at high temperature in thermophilic microorganisms. Sequences analysis shows that they share conserved cysteines and ATP binding motif (Fig. S1). Here, we report a detailed biochemical and structural characterization of TtuA that shows the presence of a [4Fe-4S] cluster essential for activity. The crystal structures of Pyrococcus horikoshii TtuA (PhTtuA) show that the cluster, chelated by only three cysteines, is adjacent to the ATP binding site. The presence of electron density near the fourth iron, nonbonded to the protein, indicates that the cluster can bind an exogenous substrate. We propose that thiolation occurs via sulfur binding to the cluster and transfer to the tRNA substrate. The fact that the catalytic [4Fe-4S] cluster serves as a sulfur carrier during a nonredox thiolation reaction illustrates an unknown function in iron-sulfur enzymology. Results m 5 s 2 U but Not s 2 C Is Present in tRNAs from Thermotoga maritima. In the Thermotoga maritima genome, only one homolog of the ttuA gene was detected (2). It was earlier suggested that TtuA could perform thiolation of both C32 and m 5 U54 in this organism (2), because both s 2 C and m 5 s 2 U were detected in bulk tRNAs (3). However, our results show that, although 10.7 m 5 s 2 U modifications per 1,000 uridines were detected, both m 5 U and s 2 C were under the threshold of detection (below one modification per million normal nucleosides) (Fig. S2). T. maritima TtuA Binds an [Fe-S] Cluster. Recombinant T. maritima TtuA (TmTtuA) was purified as an apoprotein, apo-TmTtuA (Fig. 2A and Fig. S3A), then anaerobically treated with ferrous iron and L-cysteine in the presence of a cysteine desulfurase, and finally, purified (Fig. S3B) in the form of a homogeneous dimeric brownish protein, named holo-TmTtuA. Metal analysis (1.6 ± 0.1 Zn, 3.1 ± 0.2 Fe, and 2.6 ± 0.3 S per monomer) and UV-visible as well as EPR spectroscopy (Fig. 2) show that one TmTtuA monomer binds Significance Posttranscriptional modifications of tRNA are essential for trans-lational fidelity. More specifically, mechanisms of selective sul-furation of tRNAs are still largely unknown, and the enzymes responsible for these reactions are incompletely investigated. Therefore, characterizing such systems at the molecular level is greatly valuable to our understanding of a whole class of tRNA modification reactions. We study TtuA, a representative member of a tRNA modification enzyme superfamily, and show that it intriguingly catalyzes a nonredox sulfur insertion within tRNA using a catalytically essential [4Fe-4S] cluster. This report opens perspectives regarding functions of iron-sulfur proteins in biology as well as chemical reactions catalyzed by iron-sulfur clusters.

Fluoroquinolone (FQ) antibacterials are known to exhibit photosensitization properties leading to the formation of oxidative damage to DNA. In addition, photoexcited lomefloxacin (Lome) was recently shown to induce the formation of cyclobutane pyrimidine dimers via triplet-triplet energy transfer. The present study is aimed at gaining further insights into the photosensitization mechanisms of several FQ including enoxacin (Enox), Lome, norfloxacin (Norflo) and ofloxacin (Oflo). This was achieved by monitoring the formation of DNA base degradation products upon UVA-mediated photosensitization of 2'-deoxyguanosine, isolated and cellular DNA. Oflo and Norflo act mainly via a Type-II mechanism whereas Lome and, to a lesser extent, Enox behave more like Type-I photosensitizers. However, the extent of oxidative damage was found to be relatively low. In contrast, it was found that cyclobutane thymine dimers represent the major class of damage induced by Enox, Lome and Norflo within isolated and cellular DNA upon UVA irradiation. This striking observation confirms that FQ are able to promote efficient triplet energy transfer to DNA. The levels of photosensitized formation of strand breaks, alkali-labile sites and oxidative damage to cellular DNA, as measured by the comet assay, were confirmed to be rather low. Therefore, we propose that the phototoxic effects of FQ are mostly accounted for energy transfer mechanism rather than by Type-I or -II photosensitization processes.

4-Hydroxy-2-nonenal (HNE), one of the main aldehydic compounds released during lipid peroxidation, has been proposed to react with DNA bases in cells. Several classes of DNA lesions involving addition of either HNE or its 2,3-epoxide (epox-HNE) have been identified. In the present work, HPLC associated with tandem mass spectrometry was used to determine the pattern of HNE-induced DNA lesions. First, adducts were quantified within isolated DNA treated with HNE under peroxidizing conditions. The 1,N2-propano-2'-deoxyguanosine adduct of HNE (HNE-dGuo) was found to be the major lesion under all conditions studied. 1,N6-Ethenoadenine and 1,N2-ethenoguanine together with their (1,2-dihydroxyheptyl)-substituted derivatives, which all arise from the reaction of epox-HNE with DNA, were produced in significantly lower yields, even in the presence of 20 mM H2O2. The pyrimidopurinone malondialdehyde-2'-deoxyguanosine adduct was also found to be produced, although in very low yield. Similar results were obtained in cultured human monocytes incubated with HNE, because the HNE-dGuo adduct represented more than 95% of the overall adducts to DNA. In addition, the former lesion was poorly repaired, in contrast to 1,N2-ethenoguanine and, to a lesser extent, 1,N6-ethenoadenine. Altogether, these results suggest than HNE-dGuo may represent the best biomarker of the genotoxic effects of HNE.

International audience; : DNA repair mechanisms are key components for the maintenance of the essential mitochondrial genome. Among them, base excision repair (BER) processes, dedicated in part to oxidative DNA damage, are individually well known in mitochondria. However, no large view of these systems in differential physiological conditions is available yet. Combining the use of pure mitochondrial fractions and a multiplexed oligonucleotide cleavage assay on a microarray, we demonstrated that a large range of glycosylase activities were present in Drosophila mitochondria. Most of them were quantitatively different from their nuclear counterpart. Moreover, these activities were modified during aging.

International audience; The well established toxicity of cadmium and cadmium compounds results from their additive effects on several key cellular processes, including DNA repair. Mammalian cells have evolved several biochemical pathways to repair DNA lesions and maintain genomic integrity. By interfering with the homeostasis of redox metals and antioxidant systems, cadmium promotes the development of an intracellular environment that results in oxidative DNA damage which can be mutagenic if unrepaired. Small base lesions are recognised by specialized glycosylases and excised from the DNA molecule. The resulting abasic sites are incised, and the correct sequences restored by DNA polymerases using the opposite strands as template. Bulky lesions are recognised by a different set of proteins and excised from DNA as part of an oligonucleotide. As in base repair, the resulting gaps are filled by DNA polymerases using the opposite strands as template. Thus, these two repair pathways consist in excision of the lesion followed by DNA synthesis. In this study, we analysed in vitro the direct effects of cadmium exposure on the functionality of base and nucleotide DNA repair pathways. To this end, we used recently described dedicated microarrays that allow the parallel monitoring in cell extracts of the repair activities directed against several model base and/or nucleotide lesions. Both base and nucleotide excision/repair pathways are inhibited by CdCl₂, with different sensitivities. The inhibitory effects of cadmium affect mainly the recognition and excision stages of these processes. Furthermore, our data indicate that the repair activities directed against different damaged bases also exhibit distinct sensitivities, and the direct comparison of cadmium effects on the excision of uracile in different sequences even allows us to propose a hierarchy of cadmium sensibility within the glycosylases removing U from DNA. These results indicate that, in our experimental conditions, cadmium is a very potent DNA repair poison.

DNA repair mechanisms constitute major defences against agents that cause cancer, degenerative disease and aging. Different repair systems cooperate to maintain the integrity of genetic information. Investigations of DNA repair involvement in human pathology require an efficient tool that takes into account the variety and complexity of repair systems. We have developed a highly sensitive damaged plasmid microarray to quantify cell lysate excision/synthesis (ES) capacities using small amounts of proteins. This microsystem is based on efficient immobilization and conservation on hydrogel coated glass slides of plasmid DNA damaged with a panel of genotoxic agents. Fluorescent signals are generated from incorporation of labelled dNTPs by DNA excision-repair synthesis mechanisms at plasmid sites. Highly precise DNA repair phenotypes i.e. simultaneous quantitative measures of ES capacities toward seven lesions repaired by distinct repair pathways, are obtained. Applied to the characterization of xeroderma pigmentosum (XP) cells at basal level and in response to a low dose of UVB irradiation, the assay showed the multifunctional role of different XP proteins in cell protection against all types of damage. On the other hand, measurement of the ES of peripheral blood mononuclear cells from six donors revealed significant diversity between individuals. Our results illustrate the power of such a parallelized approach with high potential for several applications including the discovery of new cancer biomarkers and the screening of chemical agents modulating DNA repair systems.

Characterization of DNA-N-glycosylase activities in cell extract is a challenging problem and could represent a major concern for medical applications. Synthetic oligonucleotides which contain base lesions located on specific sites constitute suitable substrates for their study. An in vitro miniaturized assay was developed that allows the measurement of cleavage activities of DNA repair enzymes on a set of oligonucleotides (ODNs) that contained different lesions. The modified ODNs were indirectly hybridized onto probes chemically fixed at defined sites on a circular format within each well of a 96-well microtiter plate (Oligo Sorbent Array, OLISA). The lesions were selected among oxidative damage (8-oxo-7,8-dihydroguanine, formylamine), deaminated bases (uracil, hypoxanthine) and alkylated base (N(6)-etheno-adenine). Cleavage specificity was checked using different enzymes: Fapy-DNA-N-glycosylase, 3-methyladenine DNA glycosylase II, uracil-N-glycosylase, endonuclease V and endonuclease VIII. The extent of excision could be monitored simultaneously for the selected base damage. For this purpose, we used automated fluorescence imaging analysis of the residual ODNs that contained lesions and remained on the support after release of the cleaved ODNs recognized by the repair enzymes. The results indicated that this assay could advantageously replace the analysis of glycosylase activities by PAGE techniques. Finally we show that this in vitro repair assay represents an interesting tool for the determination of cellular repair activities.

The damage profile produced by the reaction of singlet molecular oxygen with cellular DNA was determined using the comet assay associated with DNA repair enzymes. Singlet oxygen was produced intracellularly by thermal decomposition of a watersoluble endoperoxide of a naphthalene derivative which is able to penetrate through the membrane into mammalian cells. We found that the DNA modifications produced by singlet oxygen were almost exclusively oxidised purines recognised by the formamidopyrimidine DNA N-glycosylase. In contrast, significant amounts of direct strand breaks and alkalilabile sites or oxidised pyrimidines, detectable by the bacterial endonuclease III, were not produced.

BCR-ABL expression in leukemic cells is associated with several types of DNA repair abnormalities, involving homologous recombination (HR), non-homologous end joining (NHEJ), nucleotide excision repair (NER), mismatch repair (MMR) and base-excision repair (BER) pathways. These defects, combined with the genetic instability inherent to chronic myeloid leukemia (CML), are thought lead to ABL-kinase domain mutations which remain poorly repaired and selected by tyrosine kinase inhibitor (TKI) therapies, leading to drug resistance. Currently, there is no functional, practical, single step assay to determine if BCR-ABL expression in a given leukemic cell is predominantly associated with a specific DNA repair pathway. For this purpose, we have used a novel DNA repair test based on biopchips evaluating the functional capacity of cells to achieve DNA repair through the use of a functional excision/synthesis repair assay that establish DNA Repair Enzyme Signatures. This assay allows monitoring the repair of a set of DNA lesions handled by BER (8oxoG, alkylated bases, glycols and Abasic sites) and NER (photoproducts, psoralen and cisplatin adducts). For modelling CML, we have used the UT7 cell line expressing BCR-ABL and T315I-mutated BCR-ABL. Parental (P)-UT7 cells were used as controls. We have tested the effects of BCR-ABL tyrosine kinase activity on the DNA repair assays using two strategies: The first was the evaluation of the effects of the nuclear extracts of UT7 cells expressing either native (N) BCR-ABL or T315I-mutated BCR-ABL before and after incubation of the cells in the presence of Imatinib (IM) or Nilotinib whereas the second tested the effects of BCR-ABL in an inducible system without the use of TKI. As expected, UT7 cells with N-BCR-ABL were sensitive to the inhibitory effects of these drugs whereas UT7 cells with T315I-mutated BCR-ABL were totally resistant. Using this system, we have found that the inhibition of BCR-ABL by IM stimulated the DNA repair capacity of the cells and specially BER (8oxoG, alkylated bases and glycols) and NER (photoproducts and psoralen adducts) after 4 or 8 hours of treatment, as compared to baseline repair capacities ( p< 0.05). No effect was detected for the repair of Abasic sites and Cisplatin adducts. When the cells were treated with Nilotinib in the same conditions, we have observed also the stimulation of DNA repair capacities for all lesions except for the Abasic sites ( p< 0.125). The fact of treating P-UT-7 cells or UT7-T315I cells with IM or Nilotinib had no effect and led conversely, to the inhibition of DNA repair activity via Abasic and Cisplat adducts pathways (p< 0.05) or Pso (p < 0.125). To confirm directly the effect of the BCR-ABL activity in the repair modifications observed, we have used UT7 cell lines expressing N-BCR-ABL or T315I-mutated BCR-ABL under the control of a Doxycycline-inducible promoter. In this TET-OFF system, BCR-ABL expression is inhibited upon Doxycycline addition to the culture and BCR-ABL protein becomes undetectable by Western blots at day 8. In this system, the analysis of DNA repair capacity demonstrated a statistically significant stimulation of repair of Alkylated bases, Glycols, Psoralen adducts and photoproducts ( p < 0.05) upon inhibition of N-BCR-ABL or that of T315I-mutated BCR-ABL. Interestingly, the fact of reducing BCR-ABL T315I in the DOX-inducible system stimulated DNA repair capacity whereas in the non-inducible UT7 cells expressing T315I, IM did not have a stimulatory effect, whereas Nilotinib induced a slight stimulation of both NER and BER pathways after 8 hours of treatment. Overall, these results demonstrate that the novel microarrays that we describe can be efficiently detect the DNA repair ability of the leukemic cells and the reversal of these abnormalities on TKI therapies. The preliminay results suggest clearly a differential effect of IM as compared to Nilotinib in terms of the stimulation of DNA repair capacity. This new methodology can now be used to quantify the abnormality of the DNA repair pathways in CML cells at diagnosis, allowing the monitoring of the tyrosine kinase inhibitor therapies and potentially predicting the occurrence of ABL-kinase mutations according to the preferential involvement of NER or BER pathways. Disclosures Turhan: Bristol Myers Squibb, Novartis: Honoraria, Research Funding. Sauvaigo:LXRepair: Employment, Equity Ownership.