Characterization of DNA−Protein Cross-Links Induced by Oxanine: Cellular Damage Derived from Nitric Oxide and Nitrous Acid

LC-MS/MS Quantitation of Formaldehyde-Glutathione Conjugates as Biomarkers of Formaldehyde Exposure and Exposure-Induced Antioxidants: A New Look on an Old Topic

Humans are continuously exposed to formaldehyde via both endogenous and exogenous sources. Prolonged exposure to formaldehyde is associated with many human diseases, such as lung cancer and leukemia. The goal of this study is to develop biomarkers to measure formaldehyde exposure, which could be used to predict the risk of associated diseases. As glutathione (GSH) is well-known for its crucial role in the detoxification of a wide variety of xenobiotics, including formaldehyde, we rigorously quantitated in this study the conjugates formed when formaldehyde reacted with GSH using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) coupled with an isotope dilution method. The results showed for the first time that (S)-1-(((R)-2-amino-3-(carboxymethylamino)-3-oxopropylthio)methyl)-5-oxopyrrolidine-2-carboxylic acid (PGF) and thioproline-glycine (SPro-Gly) are major metabolites in both nonenzymatic reactions and formaldehyde-exposed human cells. In particular, over 35% of the formaldehyde from external sources was found to convert to SPro-Gly in the exposed cells. Interestingly, data showed that these exposure-induced adducts exhibited good antioxidative properties, which can protect cells from hydrogen peroxide mediated oxidative insult. It is anticipated that the findings of this study could shed light on developing PGF and SPro-Gly as dietary supplements and on the development of noninvasive methods to assess health risks associated with formaldehyde exposure.

Nucleobase-involved native chemical ligation: a novel reaction between an oxanine nucleobase and N-terminal cysteine for oligonucleotide-peptide conjugation

In bioconjugation chemistry, achieving a target-specific reaction for a non-modified amino acid is challenging. Here, we report a novel nucleobase-involved native chemical ligation (NbCL) that allows a site-specific oligonucleotide-peptide conjugation via a new S-N acyl transfer reaction between an oxanine nucleobase and N-terminal cysteine.

Analysis of cysteine glutathionylation in hemoglobin of gastric cancer patients using nanoflow liquid chromatography/triple-stage mass spectrometry

Glutathione is an intracellular antioxidant capable of scavenging free radicals and detoxifying electrophiles from endogenous and exogenous sources via the free thiol group. Post-translational glutathionylation at cysteine residues of proteins can affect the structure and cause a functional change of proteins. Protein glutathionylation has been proven to reflect the cellular redox status. Our previous report indicates that the levels of glutathionylation in hemoglobin from peripheral blood of smokers are significantly higher than in nonsmokers. In this study, a nanoflow liquid chromatography/nanospray ionization triple-stage mass spectrometric (nanoLC/NSI-MS³ ) method with a linear ion trap mass spectrometer was employed to quantify glutathionylated peptides in the trypsin digests of hemoglobin from gastric cancer patients. We compare the extent of glutathionylation in hemoglobin from nonsmoking gastric cancer patients with that from nonsmoking healthy adults. Using a carboxymethylated peptide as the reference peptide, the relative quantification of each glutathionylated peptide was measured as the peak area ratio of the modified peptide versus the sum of the peak areas of the modified and the carboxymethylated parent peptide in the selected reaction monitoring chromatograms. Using this method, we found that the extents of glutathionylation at Cys-104 of the α-globin and Cys-93 of β-globulin hemoglobin from 10 gastric cancer patients were significantly higher than those from 14 normal individuals with p values <0.0001. Our results suggest the possibility of using the extent of cysteine glutathionylation at β-93 of hemoglobin as an oxidative stress biomarker candidate for gastric cancer.

When DNA repair goes wrong: BER-generated DNA-protein crosslinks to oxidative lesions

Free radicals generate an array of DNA lesions affecting all parts of the molecule. The damage to deoxyribose receives less attention than base damage, even though the former accounts for ∼20% of the total. Oxidative deoxyribose fragments (e.g., 3'-phosphoglycolate esters) are removed by the Ape1 AP endonuclease and other enzymes in mammalian cells to enable DNA repair synthesis. Oxidized abasic sites are initially incised by Ape1, thus recruiting these lesions into base excision repair (BER) pathways. Lesions such as 2-deoxypentos-4-ulose can be removed by conventional (single-nucleotide) BER, which proceeds through a covalent Schiff base intermediate with DNA polymerase β (Polβ) that is resolved by hydrolysis. In contrast, the lesion 2-deoxyribonolactone (dL) must be processed by multinucleotide ("long-patch") BER: attempted repair via the single-nucleotide pathway leads to a dead-end, covalent complex with Polβ cross- linked to the DNA by an amide bond. We recently detected these stable DNA-protein crosslinks (DPC) between Polβ and dL in intact cells. The features of the DPC formation in vivo are exactly in keeping with the mechanistic properties seen in vitro: Polβ-DPC are formed by oxidative agents in line with their ability to form the dL lesion; they are not formed by non-oxidative agents; DPC formation absolutely requires the active-site lysine-72 that attacks the 5'-deoxyribose; and DPC formation depends on Ape1 to incise the dL lesion first. The Polβ-DPC are rapidly processed in vivo, the signal disappearing with a half-life of 15-30min in both mouse and human cells. This removal is blocked by inhibiting the proteasome, which leads to the accumulation of ubiquitin associated with the Polβ-DPC. While other proteins (e.g., topoisomerases) also form DPC under these conditions, 60-70% of the trapped ubiquitin depends on Polβ. The mechanism of ubiquitin targeting to Polβ-DPC, the subsequent processing of the expected 5'-peptidyl-dL, and the biological consequences of unrepaired DPC are important to assess. Many other lyase enzymes that attack dL can also be trapped in DPC, so the processing mechanisms may apply quite broadly.

Characterization of the deoxyguanosine-lysine cross-link of methylglyoxal

Methylglyoxal is a mutagenic bis-electrophile that is produced endogenously from carbohydrate precursors. Methylglyoxal has been reported to induce DNA-protein cross-links (DPCs) in vitro and in cultured cells. Previous work suggests that these cross-links are formed between guanine and either lysine or cysteine side chains. However, the chemical nature of the methylglyoxal induced DPC have not been determined. We have examined the reaction of methylglyoxal, deoxyguanosine (dGuo), and Nα-acetyllysine (AcLys) and determined the structure of the cross-link to be the N2-ethyl-1-carboxamide with the lysine side chain amino group (1). The cross-link was identified by mass spectrometry and the structure confirmed by comparison to a synthetic sample. Further, the cross-link between methylglyoxal, dGuo, and a peptide (AcAVAGKAGAR) was also characterized. The mechanism of cross-link formation is likely to involve an Amadori rearrangement.

Mapping the binding site of snurportin 1 on native U1 snRNP by cross-linking and mass spectrometry

Mass spectrometry allows the elucidation of molecular details of the interaction domains of the individual components in macromolecular complexes subsequent to cross-linking of the individual components. Here, we applied chemical and UV cross-linking combined with tandem mass-spectrometric analysis to identify contact sites of the nuclear import adaptor snurportin 1 to the small ribonucleoprotein particle U1 snRNP in addition to the known interaction of m₃G cap and snurportin 1. We were able to define previously unknown sites of protein–protein and protein–RNA interactions on the molecular level within U1 snRNP. We show that snurportin 1 interacts with its central m₃G-cap-binding domain with Sm proteins and with its extreme C-terminus with stem-loop III of U1 snRNA. The crosslinking data support the idea of a larger interaction area between snurportin 1 and U snRNPs and the contact sites identified prove useful for modeling the spatial arrangement of snurportin 1 domains when bound to U1 snRNP. Moreover, this suggests a functional nuclear import complex that assembles around the m₃G cap and the Sm proteins only when the Sm proteins are bound and arranged in the proper orientation to the cognate Sm site in U snRNA.

Oxidative stress in diabetes and Alzheimer's disease

Oxidative stress plays a major role in diabetes as well as in Alzheimer's disease and other related neurological diseases. Intracellular oxidative stress arises due to the imbalance in the production of reactive oxygen/reactive nitrogen species and cellular antioxidant defense mechanisms. In turn, the excess reactive oxygen/reactive nitrogen species mediate the damage of proteins and nucleic acids, which have been shown to have direct and deleterious consequences in diabetes and Alzheimer's disease. Oxidative stress also contributes to the production of advanced glycation end products through glycoxidation and lipid peroxidation. The advanced glycation end products and lipid peroxidation products are ubiquitous to diabetes and Alzheimer's disease and serve as markers of disease progression in both disorders. Antioxidants and advanced glycation end products inhibitors, either induced endogenously or exogenously introduced, may counteract with the deleterious effects of the reactive oxygen/reactive nitrogen species and thereby, in prevention or treatment paradigms, attenuate or substantially delay the onset of these devastating pathologies.

Investigation of DNA-protein cross-link formation between lysozyme and oxanine by mass spectrometry

Reactive nitrogen species are implicated in inflammatory diseases and cancers. Oxanine (Oxa) is a DNA lesion product originating from the guanine base through exposure to nitric oxide, nitrous acid, or N-nitrosoindoles. Oxanine was found to mediate formation of DNA-protein cross-links (DPCs) in the cell extract. We have previously characterized two DNA-protein cross-links from the reaction between Oxa and glutathione: namely, the thioester and the amide. In this study, lysozyme was used to study site-specific modification on protein by Oxa moieties in DNA. With the aid of nanoLC coupled with nanospray ionization tandem mass spectrometry, addition of Oxa was found at Lys13, Lys97, Lys116, Ser85, and Ser86 of lysozyme when it was treated with 2'-deoxyoxanosine (dOxo). Furthermore, incubation of lysozyme with Oxa-containing calf thymus DNA, produced by treating DNA with nitrous acid, led to lysozyme modification at Lys116, Ser85, and Ser86. Interestingly, none of the cysteine residues was modified by dOxo, in contrast with our previous findings that dOxo reacted with oxidized glutathione disulfide, forming the thioester. This might be due to the half-life of the dOxo-derived thioester being 2.2 days at the pH of incubation. Furthermore, the sites of modifications on lysozyme are in good agreement with the solvent accessibility of the residues. Since repair of Oxa-derived DPCs has not been extensively investigated, these results suggest that these stable DPCs might represent important forms of cellular damage caused by reactive nitrogen species involved in inflammationrelated diseases.