Nitric oxide and peroxynitrite. The ugly,the uglier and the not so good

Nitric oxide, a gaseous free radical, is poorly reactive with most biomolecules but highly reactive with other free radicals. Its ability to scavenge peroxyl and other damaging radicals may make it an important antioxidant in vivo, particular in the cardiovascular system, although this ability has been somewhat eclipsed in the literature by a focus on the toxicity of peroxynitrite, generated by reaction of O^·-₂ with NO^· (or of NO^- with O₂). On balance, experimental and theoretical data support the view that ONOO^- can lead to hydroxyl radical (OH^·) generation at pH 7.4, but it seems unlikely that OH^· contributes much to the cytotoxicity of ONOO^-. The cytotoxicity of ONOO^- may have been over-emphasized: its formation and rapid reaction with antioxidants may provide a mechanism of using NO^· to dispose of excess O^·-₂, or even of using O^·-₂ to dispose of excess NO^·, in order to maintain the correct balance between these radicals in vivo. Injection or instillation of “bolus” ONOO^- into animals has produced tissue injury, however, although more experiments generating ONOO^- at steady rates in vivo are required. The presence of 3-nitrotyrosine in tissues is still frequently taken as evidence of ONOO^- generation in vivo, but abundant evidence now exists to support the view that it is a biomarker of several “reactive nitrogen species”. Another under-addressed problem is the reliability of assays used to detect and measure 3-nitrotyrosine in tissues and body fluids: immunostaining results vary between laboratories and simple HPLC methods are susceptible to artefacts. Exposure of biological material to low pH (e.g. during acidic hydrolysis to liberate nitrotyrosine from proteins) or to H₂O₂ might cause artefactual generation of nitrotyrosine from NO^-₂ in the samples. This may be the origin of some of the very large values for tissue nitrotyrosine levels quoted in the literature. Nitrous acid causes not only tyrosine nitration but also DNA base deamination at low pH: these events are relevant to the human stomach since saliva and many foods are rich in nitrite. Several plant phenolics inhibit nitration and deamination in vitro, an effect that could conceivably contribute to their protective effects against gastric cancer development.     

Prototropic tautomerism and basic molecular principles of hypoxanthine mutagenicity: an exhaustive quantum-chemical analysis

The molecular structures, relative stability order, and dipole moments of a complete family of 21 planar hypoxanthine (Hyp) prototropic molecular–zwitterionic tautomers including ylidic forms were computationally investigated at the MP2/6–311++G(2df,pd)//B3LYP/6–311++G(d,p) level of theory in vacuum and in three different surrounding environments: continuum with a low dielectric constant (??=?4) corresponding to a hydrophobic interface of protein–nucleic acid interactions, dimethylsulfoxide (DMSO), and water. The keto-N1HN7H tautomer was established to be the global minimum in vacuum and in continuum with ??=?4, while Hyp molecule exists as a mixture of the keto-N1HN9H and keto-N1HN7H tautomers in approximately equal amounts in DMSO and in water at T?=?298.15?K. We found out that neither intramolecular tautomerization by single proton transfer in the Hyp base, nor intermolecular tautomerization by double proton transfer in the most energetically favorable Hyp·Hyp homodimer (symmetry C _2h ), stabilized by two equivalent N1H…O6 H-bonds, induces the formation of the enol tautomer (marked with an asterisk) of Hyp with cis-oriented O6H hydroxyl group relative to neighboring N1C6 bond. We first discovered a new scenario of the keto–enol tautomerization of Hyp?·?Hyp homodimer (C _2h ) via zwitterionic near-orthogonal transition state (TS), stabilized by N1⁺H…N1^? and O6⁺H…N1^? H-bonds, to heterodimer Hyp^??·?Hyp (C _s ), stabilized by O6H…O6 and N1H…N1 H-bonds. We first showed that Hyp^??·?Thy mispair (C _s ), stabilized by O6H…O4, N3H…N1, and C2H…O2 H-bonds, mimicking Watson–Crick base pairing, converts to the wobble Hyp?·?Thy base pair (C _s ), stabilized by N3H…O6 and N1H…O2 H-bonds, via high- and low-energy TSs and intermediate Hyp?·?Thy^?, stabilized by O4H…O6, N1H…N3, and C2H…O2 H-bonds. The most energetically favorable TS is the zwitterionic pair Hyp⁺?·?Thy^? (C _s ), stabilized by O6⁺H…O4^?, O6⁺H…N3^?, N1⁺H…N3^?, and N1⁺H…O2^? H-bonds. The authors expressed and substantiated the hypothesis, that the keto tautomer of Hyp is a mutagenic compound, while enol tautomer Hyp^? does not possess mutagenic properties. The lifetime of the nonmutagenic tautomer Hyp^? exceeds by many orders the time needed to complete a round of DNA replication in the cell. For the first time purine–purine planar H-bonded mispairs containing Hyp in the anti-orientation with respect to the sugar moiety – Hyp?·?Ade _syn , Hyp?·?Gua^? _syn , and Hyp?·?Gua _syn , that closely resembles the geometry of the Watson–Crick base pairs, have been suggested as the source of transversions. An influence of the surrounding environment (??=?4) on the stability of studied complexes and corresponding TSs was estimated by means of the conductor-like polarizable continuum model. Electron-topological, structural, vibrational, and energetic characterictics of all conventional and nonconventional H-bonds in the investigated structures are presented. Presented data are key to understanding elementary molecular mechanisms of mutagenic action of Hyp as a product of the adenine deamination in DNA.     

Measurement of deaminated cytosine adducts in DNA using a novel hybrid thymine DNA glycosylase

The hydrolytic deamination of cytosine and 5-methylcytosine drives many of the transition mutations observed in human cancer. The deamination-induced mutagenic intermediates include either uracil or thymine adducts mispaired with guanine. While a substantial array of methods exist to measure other types of DNA adducts, the cytosine deamination adducts pose unusual analytical problems, and adequate methods to measure them have not yet been developed. We describe here a novel hybrid thymine DNA glycosylase (TDG) that is comprised of a 29-amino acid sequence from human TDG linked to the catalytic domain of a thymine glycosylase found in an archaeal thermophilic bacterium. Using defined-sequence oligonucleotides, we show that hybrid TDG has robust mispair-selective activity against deaminated U:G and T:G mispairs. We have further developed a method for separating glycosylase-released free bases from oligonucleotides and DNA followed by GC–MS/MS quantification. Using this approach, we have measured for the first time the levels of total uracil, U:G, and T:G pairs in calf thymus DNA. The method presented here will allow the measurement of the formation, persistence, and repair of a biologically important class of deaminated cytosine adducts.     

Thermal resistance of UV-mutagenesis to photoreactivation in E. coli B/r uvrA ung: estimate of activation energy and further analysis

Summary Ultraviolet light (UV) induced mutations in the glnU and glnV ^utRNA genes in Escherichia coli are thought to be targeted by UV photoproducts. In a previous study with a uracil-DNA glycosylase deficient strain, UV-induced glnU ^oand glnV ^otRNA suppressor mutations became resistant to photoreactivation (PR) following thermal treatment. It was proposed that deamination of cytosine in the cytosine-containing cyclobutyl dimers at the sites of these suppressor mutations produced uracil residues in sequence upon PR. In the absence of glycosylase, the C U conversion yielded the requisite G:C A:T transitions. In the present study, this thermal resistance of UV-mutagenesis to PR is characterized. It is dependent on the initial UV-fluence and temperature of holding but not on the UmuC⁺ gene product. The data obtained yield an estimate of an activation energy of 17±3 kcal/mol for the deamination of cytosines contained in dimers. This compares to 29 kcal/mol for unaffected cytosines in DNA. In addition, an estimate of the probability of cyclobutyl dimer formation at the target sites for glnU ^oand glnV ^osuppressor mutations indicate that these lesions can not entirely account for the mutation frequencies recovered in the absence of PR. This is interpreted as an indication that, in addition to thyminecytosine cyclobutyl dimers, other UV-induced lesions, possibly Thy(6-4)Cyt photoproducts, may also target glnU ^oand glnV ^osuppressor mutations.     

Mechanism of dTTP inhibition of the bifunctional dCTP deaminase:dUTPase encoded by Mycobacterium tuberculosis

Recombinant deoxycytidine triphosphate (dCTP) deaminase from Mycobacterium tuberculosis was produced in Escherichia coli and purified. The enzyme proved to be a bifunctional dCTP deaminase:deoxyuridine triphosphatase. As such, the M. tuberculosis enzyme is the second bifunctional enzyme to be characterised and provides evidence for bifunctionality of dCTP deaminase occurring outside the Archaea kingdom. A steady-state kinetic analysis revealed that the affinity for dCTP and deoxyuridine triphosphate as substrates for the synthesis of deoxyuridine monophosphate were very similar, a result that contrasts that obtained previously for the archaean Methanocaldococcus jannaschii enzyme, which showed approximately 10-fold lower affinity for deoxyuridine triphosphate than for dCTP.The crystal structures of the enzyme in complex with the inhibitor, thymidine triphosphate, and the apo form have been solved. Comparison of the two shows that upon binding of thymidine triphosphate, the disordered C-terminal arranges as a lid covering the active site, and the enzyme adapts an inactive conformation as a result of structural changes in the active site. In the inactive conformation dephosphorylation cannot take place due to the absence of a water molecule otherwise hydrogen-bonded to O2 of the α-phosphate.     

Comments on `Concentration by Evaporation and the Prebiotic Synthesis of Cytosine'

The claim by Nelson et al. (2001) that the reactionof cyanoacetaldehyde and urea provides `an efficient prebioticsynthesis' of cytosine is disputed. The authors have not dealt withthe important points presented in a criticism of this reaction(Shapiro, 1999): (1) The reactants undergo side reactions with commonnucleophiles that appear to proceed more rapidly than cytosineformation, and (2) No reactions have been described thus far thatwould produce cytosine at a rate sufficient to compensate for itsdecomposition by deamination, and permit accumulation over extendedperiods of time. Instead, Nelson et al. have conducted `drying-down' experiments, inan effort to simulate evaporations on the early Earth, but thedesign of these experiments is flawed. The initial reactantconcentrations are much higher than might be expected in a naturalsetting, and potentially interfering substances such as glycine,cyanide and thiols have been excluded. `Drying beaches and dryinglagoons' have been invoked as sites for such a reaction but noeffort has been made to describe the characteristics of such sitesor to estimate their frequency with reference to the present Earth.In the absence of contradictory data, the conclusion put forward inShapiro (1999) remains valid: `It was quite unlikely that cytosineplayed a role in the origin of life'.     

Theoretical insights into the protonation states of active site cysteine and citrullination mechanism of Porphyromonas gingivalis peptidylarginine deiminase

Porphyromonas gingivalis peptidylarginine deiminase (PPAD) catalyzes the citrullination of peptidylarginine, which plays a critical role in the rheumatoid arthritis (RA) and gene regulation. For a better understanding of citrullination mechanism of PPAD, it is required to establish the protonation states of active site cysteine, which is still a controversial issue for the members of guanidino‐group‐modifying enzyme superfamily. In this work, we first explored the transformation between the two states: State N (both C351 and H236 are neutral) and State I (both residues exist as a thiolate–imidazolium ion pair), and then investigated the citrullination reaction of peptidylarginine, using a combined QM/MM approach. State N is calculated to be more stable than State I by 8.46 kcal/mol, and State N can transform to State I via two steps of substrate‐assisted proton transfer. Citrullination of the peptidylarginine contains deamination and hydrolysis. Starting from State N, the deamination reaction corresponds to an energy barrier of 18.82 kcal/mol. The deprotonated C351 initiates the nucleophilic attack to the substrate, which is the key step for deamination reaction. The hydrolysis reaction contains two chemical steps. Both the deprotonated D238 and H236 can act as the bases to activate the hydrolytic water, which correspond to similar energy barriers (～17 kcal/mol). On the basis of our calculations, C351, D238, and H236 constitute a catalytic triad, and their protonation states are critical for both the deamination and hydrolysis processes. In view of the sequence similarity, these findings may be shared with human PAD1–PAD4 and other guanidino‐group‐modifying enzymes. Proteins 2017; 85:1518–1528. © 2017 Wiley Periodicals, Inc.     

Trophic discrimination factor of nitrogen isotopes within amino acids in the dobsonfly Protohermes grandis (Megaloptera: Corydalidae) larvae in a controlled feeding experiment

The trophic discrimination factor (TDF) of nitrogen isotopes (¹⁵N/¹⁴N) within amino acids, between a stream‐dwelling dobsonfly larva (Protohermes grandis: Megaloptera; Corydalidae) and its diet (chironomid larvae), was determined in controlled feeding experiments. Last‐instar larvae of P. grandis were collected from the Yozawa‐gawa River, central Japan, and reared in the laboratory. After fed to satiation for 1 month, one group of larvae was each fed one living chironomid larva per day for 4 weeks, while a second group was starved for 8 weeks. The larvae were harvested at intervals and the nitrogen isotopic composition of glutamic acid (δ¹⁵N_Glu) and phenylalanine (δ¹⁵N_Phe) were determined to calculate TDF. The mean TDF of satiated and starved larvae were 7.1‰ ± 0.5‰ (n = 3) and 7.3‰ ± 0.5‰ (n = 5), respectively. Thus, the TDF for P. grandis larvae in this study was similar to that reported for other arthropods (approximately 7‰) and was independent of satiation or starvation. A previous study of wild P. grandis larvae, based on the δ¹⁵N_Glu and δ¹⁵N_Phe values, estimated its trophic position (TP) as approximately 2.0 ± 0.1 (n = 5), a low value close to that of algivores, although they are generally characterized as carnivores (usually accepted as TP ≥ 3). The TDF for P. grandis larvae suggests that their low TPs in nature were caused by incorporation of vascular plant‐derived amino acids (with a different δ¹⁵N profile from that of algae) and not by an unusually low TDF or by the effects of the satiation/starvation on amino acid metabolism.     

Structural basis for recognition and catalysis by the bifunctional dCTP deaminase and dUTPase from Methanococcus jannaschii

Potentially mutagenic uracil-containing nucleotide intermediates are generated by deamination of dCTP, either spontaneously or enzymatically as the first step in the conversion of dCTP to dTTP. dUTPases convert dUTP to dUMP, thus avoiding the misincorporation of dUTP into DNA and creating the substrate for the next enzyme in the dTTP synthetic pathway, thymidylate synthase. Although dCTP deaminase and dUTPase activities are usually found in separate but homologous enzymes, the hyperthermophile Methanococcus jannaschii has an enzyme, DCD-DUT, that harbors both dCTP deaminase and dUTP pyrophosphatase activities. DCD-DUT has highest activity on dCTP, followed by dUTP, and dTTP inhibits both the deaminase and pyrophosphatase activities. To help clarify structure-function relationships for DCD-DUT, we have determined the crystal structure of the wild-type DCD-DUT protein in its apo form to 1.42A and structures of DCD-DUT in complex with dCTP and dUTP to resolutions of 1.77A and 2.10A, respectively. To gain insights into substrate interactions, we complemented analyses of the experimentally defined weak density for nucleotides with automated docking experiments using dCTP, dUTP, and dTTP. DCD-DUT is a hexamer, unlike the homologous dUTPases, and its subunits contain several insertions and substitutions different from the dUTPase beta barrel core that likely contribute to dCTP specificity and deamination. These first structures of a dCTP deaminase reveal a probable role for an unstructured C-terminal region different from that of the dUTPases and possible mechanisms for both bifunctional enzyme activity and feedback inhibition by dTTP.     

Sulfoacetate generated by Rhodopseudomonas palustris from taurine

Genes thought to encode (a) the regulator of taurine catabolism under carbon-limiting or nitrogen-limiting conditions and (b) taurine dehydrogenase were found in the genome of Rhodopseudomonas palustris. The organism utilized taurine quantitatively as a sole source of nitrogen (but not of carbon) for aerobic and photoheterotrophic growth. No sulfate was released, and the C-sulfonate bond was recovered stoichiometrically as sulfoacetate, which was identified by mass spectrometry. An inducible sulfoacetaldehyde dehydrogenase was detected. R. palustris thus contains a pathway to generate a natural product that was previously believed to be formed solely from sulfoquinovose.The senior author (AMC) would like to express his thanks for the rewarding experience of doing postdoctoral research in the laboratory of Prof. H.-G. Schlegel.