Excision of 5-Carboxylcytosine by Thymine DNA Glycosylase

5-Methylcytosine (mC) is an epigenetic mark that is written by methyltransferases, erased through passive and active mechanisms, and impacts transcription, development, diseases including cancer, and aging. Active DNA demethylation involves TET-mediated stepwise oxidation of mC to 5-hydroxymethylcytosine, 5-formylcytosine (fC), or 5-carboxylcytosine (caC), excision of fC or caC by thymine DNA glycosylase (TDG), and subsequent base excision repair. Many elements of this essential process are poorly defined, including TDG excision of caC. To address this problem, we solved high-resolution structures of human TDG bound to DNA with cadC (5-carboxyl-2'-deoxycytidine) flipped into its active site. The structures unveil detailed enzyme-substrate interactions that mediate recognition and removal of caC, many involving water molecules. Importantly, two water molecules contact a carboxylate oxygen of caC and are poised to facilitate acid-catalyzed caC excision. Moreover, a substrate-dependent conformational change in TDG modulates the hydrogen bond interactions for one of these waters, enabling productive interaction with caC. An Asn residue (N191) that is critical for caC excision is found to contact N3 and N4 of caC, suggesting a mechanism for acid-catalyzed base excision that features an N3-protonated form of caC but would be ineffective for C, mC, or hmC. We also investigated another Asn residue (N140) that is catalytically essential and strictly conserved in the TDG-MUG enzyme family. A structure of N140A-TDG bound to cadC DNA provides the first high-resolution insight into how enzyme-substrate interactions, including water molecules, are impacted by depleting the conserved Asn, informing its role in binding and addition of the nucleophilic water molecule.

Defining the Role of Nucleotide Flipping in Enzyme Specificity Using 19F NMR

A broad range of proteins employ nucleotide flipping to recognize specific sites in nucleic acids, including DNA glycosylases, which remove modified nucleobases to initiate base excision repair. Deamination, a pervasive mode of damage, typically generates lesions that are recognized by glycosylases as being foreign to DNA. However, deamination of 5-methylcytosine (mC) generates thymine, a canonical DNA base, presenting a challenge for damage recognition. Nevertheless, repair of mC deamination is important because the resulting G·T mispairs cause C → T transition mutations, and mC is abundant in all three domains of life. Countering this threat are three types of glycosylases that excise thymine from G·T mispairs, including thymine DNA glycosylase (TDG). These enzymes must minimize excision of thymine that is not generated by mC deamination, in A·T pairs and in polymerase-generated G·T mispairs. TDG preferentially removes thymine from DNA contexts in which cytosine methylation is prevalent, including CG and one non-CG site. This remarkable context specificity could be attained through modulation of nucleotide flipping, a reversible step that precedes base excision. We tested this idea using fluorine NMR and DNA containing 2'-fluoro-substituted nucleotides. We find that dT nucleotide flipping depends on DNA context and is efficient only in contexts known to feature cytosine methylation. We also show that a conserved Ala residue limits thymine excision by hindering nucleotide flipping. A linear free energy correlation reveals that TDG attains context specificity for thymine excision through modulation of nucleotide flipping. Our results provide a framework for characterizing nucleotide flipping in nucleic acids using ¹⁹F NMR.

Structural basis of damage recognition by thymine DNA glycosylase: Key roles for N-terminal residues

Thymine DNA Glycosylase (TDG) is a base excision repair enzyme functioning in DNA repair and epigenetic regulation. TDG removes thymine from mutagenic G·T mispairs arising from deamination of 5-methylcytosine (mC), and it processes other deamination-derived lesions including uracil (U). Essential for DNA demethylation, TDG excises 5-formylcytosine and 5-carboxylcytosine, derivatives of mC generated by Tet (ten-eleven translocation) enzymes. Here, we report structural and functional studies of TDG^82-308, a new construct containing 29 more N-terminal residues than TDG^111-308, the construct used for previous structures of DNA-bound TDG. Crystal structures and NMR experiments demonstrate that most of these N-terminal residues are disordered, for substrate- or product-bound TDG^82-308 Nevertheless, G·T substrate affinity and glycosylase activity of TDG^82-308 greatly exceeds that of TDG^111-308 and is equivalent to full-length TDG. We report the first high-resolution structures of TDG in an enzyme-substrate complex, for G·U bound to TDG^82-308 (1.54 Å) and TDG^111-308 (1.71 Å), revealing new enzyme-substrate contacts, direct and water-mediated. We also report a structure of the TDG^82-308 product complex (1.70 Å). TDG^82-308 forms unique enzyme-DNA interactions, supporting its value for structure-function studies. The results advance understanding of how TDG recognizes and removes modified bases from DNA, particularly those resulting from deamination.

Thymine DNA glycosylase exhibits negligible affinity for nucleobases that it removes from DNA

Thymine DNA Glycosylase (TDG) performs essential functions in maintaining genetic integrity and epigenetic regulation. Initiating base excision repair, TDG removes thymine from mutagenic G·T mispairs caused by 5-methylcytosine (mC) deamination and other lesions including uracil (U) and 5-hydroxymethyluracil (hmU). In DNA demethylation, TDG excises 5-formylcytosine (fC) and 5-carboxylcytosine (caC), which are generated from mC by Tet (ten–eleven translocation) enzymes. Using improved crystallization conditions, we solved high-resolution (up to 1.45 Å) structures of TDG enzyme–product complexes generated from substrates including G·U, G·T, G·hmU, G·fC and G·caC. The structures reveal many new features, including key water-mediated enzyme–substrate interactions. Together with nuclear magnetic resonance experiments, the structures demonstrate that TDG releases the excised base from its tight product complex with abasic DNA, contrary to previous reports. Moreover, DNA-free TDG exhibits no significant binding to free nucleobases (U, T, hmU), indicating a K_d >> 10 mM. The structures reveal a solvent-filled channel to the active site, which might facilitate dissociation of the excised base and enable caC excision, which involves solvent-mediated acid catalysis. Dissociation of the excised base allows TDG to bind the beta rather than the alpha anomer of the abasic sugar, which might stabilize the enzyme–product complex.

Coordination of MYH DNA glycosylase and APE1 endonuclease activities via physical interactions

MutY homologue (MYH) is a DNA glycosylase which excises adenine paired with the oxidative lesion 7,8-dihydro-8-oxoguanine (8-oxoG, or G(o)) during base excision repair (BER). Base excision by MYH results in an apurinic/apyrimidinic (AP) site in the DNA where the DNA sugar-phosphate backbone remains intact. A key feature of MYH activity is its physical interaction and coordination with AP endonuclease I (APE1), which subsequently nicks DNA 5' to the AP site. Because AP sites are mutagenic and cytotoxic, they must be processed by APE1 immediately after the action of MYH glycosylase. Our recent reports show that the interdomain connector (IDC) of human MYH (hMYH) maintains interactions with hAPE1 and the human checkpoint clamp Rad9-Rad1-Hus1 (9-1-1) complex. In this study, we used NMR chemical shift perturbation experiments to determine hMYH-binding site on hAPE1. Chemical shift perturbations indicate that the hMYH IDC peptide binds to the DNA-binding site of hAPE1 and an additional site which is distal to the APE1 DNA-binding interface. In these two binding sites, N212 and Q137 of hAPE1 are key mediators of the MYH/APE1 interaction. Intriguingly, despite the fact that hHus1 and hAPE1 both interact with the MYH IDC, hHus1 does not compete with hAPE1 for binding to hMYH. Rather, hHus1 stabilizes the hMYH/hAPE1 complex both in vitro and in cells. This is consistent with a common theme in BER, namely that the assembly of protein-DNA complexes enhances repair by efficiently coordinating multiple enzymatic steps while simultaneously minimizing the release of harmful repair intermediates.

The crystal structure of human quinolinic acid phosphoribosyltransferase in complex with its inhibitor phthalic acid

Quinolinic acid (QA), a biologically potent but neurodestructive metabolite is catabolized by quinolinic acid phosphoribosyltransferase (QPRT) in the first step of the de novo NAD(+) biosynthesis pathway. This puts QPRT at the junction of two different pathways, that is, de novo NAD(+) biosynthesis and the kynurenine pathway of tryptophan degradation. Thus, QPRT is an important enzyme in terms of its biological impact and its potential as a therapeutic target. Here, we report the crystal structure of human QPRT bound to its inhibitor phthalic acid (PHT) and kinetic analysis of PHT inhibition of human QPRT. This structure, determined at 2.55 Å resolution, shows an elaborate hydrogen bonding network that helps in recognition of PHT and consequently its substrate QA. In addition to this hydrogen bonding network, we observe extensive van der Waals contacts with the PHT ring that might be important for correctly orientating the substrate QA during catalysis. Moreover, our crystal form allows us to observe an intact hexamer in both the apo- and PHT-bound forms in the same crystal system, which provides a direct comparison of unique subunit interfaces formed in hexameric human QPRT. We call these interfaces "nondimeric interfaces" to distinguish them from the typical dimeric interfaces observed in all QPRTs. We observe significant changes in the nondimeric interfaces in the QPRT hexamer upon binding PHT. Thus, the new structural and functional features of this enzyme we describe here will aid in understanding the function of hexameric QPRTs, which includes all eukaryotic and select prokaryotic QPRTs.

Acute paediatric compartment syndrome of the hand caused by hereditary angiooedema

Compartment syndrome of the leg and forearm are well described in the literature. However, compartment syndrome of the hand is rare and in children it is even rarer. Atraumatic hand compartment syndrome has not to our knowledge been previously reported. We describe a case of an atraumatic compartment syndrome of the hand in a child who underwent an urgent fasciotomy. The child was diagnosed with hereditary angiooedema. We highlight a rare but serious complication of a hereditary disease not commonly seen by the surgical community. We hope that this report raises the awareness of this condition, thereby reducing delays in reaching a prompt diagnosis.

Acute myocardial infarction: profile and management at a tertiary care hospital in Karachi

OBJECTIVE

Acute Myocardial Infarction (AMI) is a rising epidemic in developing countries. While studies in the West have established the characteristics and management of AMI patients, comprehensive data reflecting these issues in the Pakistani subjects is scarce. This study examined the profile and management of AMI in patients hospitalized at a tertiary care hospital in Karachi, Pakistan.

METHODS

Three hundred forty four patients admitted in 1998 with the diagnosis of AMI met our inclusion criteria. Data on presentation, investigations, monitoring and therapy was obtained. Chi-square and t tests were used to analyze the data.

RESULTS

Out of 344 patients with AMI, 71% were males; 58% had a Q wave MI. Majority of the patients who presented within 2 hours of symptom onset (36%), had chest pain. Patients with dyspnea and no chest pain were more likely to present after 12 hours of the onset of symptoms. In-house mortality was found to be 10.8%. Low HDL and diabetes was associated with in-hospital complications. Twenty nine percent of patients were given thrombolytic therapy with a mean door-to-needle time of 1 hour 36 minutes; 33% of patients who were eligible of Streptokinase did not receive it. Cardiac catheterization was performed in 28% patients. Echocardiography and Exercise Tolerance Test, both under utilized, were performed in 67% and 16% of patients, respectively. Two hundred sixteen (70%) patients discharged from hospital were contacted via telephone and the 1-year mortality rate among them was 28%.

CONCLUSION

The profile and management of AMI was in coherence with earlier, Western studies. Chest pain units need to be established in the Emergency Room. Patients should be risk stratified prior to discharge. Public awareness regarding primary and secondary prevention and symptoms of AMI needs to be increased.

In vitro germicidal activity of teat dips against Nocardia asteroides and other udder pathogens

Nine commercial teat dip formulations containing 1.94% linear dodecylbenzene sulfonic acid, or 1% available iodine from nonylphenoxypoly (ethyleneoxy) ethanol-iodine complex, or .5% chlorhexidine acetate were tested for contamination with aerobic and anaerobic bacteria and their in vitro germicidal activity against Staphylococcus aureus, Streptococcus agalactiae, Escherichia coli, and Nocardia asteroides. All products were free of bacteria when neutralized samples were tested on blood agar or liquid thioglycollate media. To test for in vitro efficacy, each teat dip preparation was mixed with a suspension of one of the pathogenic test organisms containing 10(8) bacteria/ml (final concentration) for .5 to 15 min. Viable bacteria were evaluated by direct plating of neutralized aliquots and by filtration techniques. All products were effective against E. coli, Staph. aureus, and Strep. agalactiae. With N. asteroides, the direct plating method gave equivocal results. The filtration experiments indicated that all teat dips containing dodecylbenzene sulfonic acid and nonylphenoxypoly (ethyleneoxy) ethanol-iodine complex were effective against all four pathogens. Three of the teat dips containing chlorhexidine acetate were ineffective against N. asteroides. The fourth teat dip, containing chlorhexidine acetate and an emollient, was partially effective.

[Droperidol, seduxen, fentanyl: a study of immune reactions in vitro]

Clinical concentration of droperidol, seduxen, fentanyl were studied for their effects on in vitro immunity reaction with lymphocytes from donors and patients with lung carcinoma. In the donors, the agents caused no changes in E- and EAC-rosette formation. In the patients with lung carcinoma, droperidol elevated the number of theophylline-sensitive T lymphocytes, lowered theophylline-resistant ones and eventually normalized a theophylline-resistant to theophylline-sensitive T cell ratio. Fentanyl, 5 ng/ml was demonstrated to increase amounts of early T lymphocytes. Fentanyl concentrations (5 and 25 ng/ml) decreased B lymphocytes. It was concluded that droperidol produced a positive action and fentanyl showed heterogeneous effects on E- and EAC-rosette formation in patients with lung carcinoma.