Structural Insights into the Mechanism of Base Excision by MBD4

DNA glycosylases remove damaged or modified nucleobases by cleaving the N-glycosyl bond and the correct nucleotide is restored through subsequent base excision repair. In addition to excising threatening lesions, DNA glycosylases contribute to epigenetic regulation by mediating DNA demethylation and perform other important functions. However, the catalytic mechanism remains poorly defined for many glycosylases, including MBD4 (methyl-CpG binding domain IV), a member of the helix-hairpin-helix (HhH) superfamily. MBD4 excises thymine from G·T mispairs, suppressing mutations caused by deamination of 5-methylcytosine, and it removes uracil and modified uracils (e.g., 5-hydroxymethyluracil) mispaired with guanine. To investigate the mechanism of MBD4 we solved high-resolution structures of enzyme-DNA complexes at three stages of catalysis. Using a non-cleavable substrate analog, 2′-deoxy-pseudouridine, we determined the first structure of an enzyme-substrate complex for wild-type MBD4, which confirms interactions that mediate lesion recognition and suggests that a catalytic Asp, highly conserved in HhH enzymes, binds the putative nucleophilic water molecule and stabilizes the transition state. Observation that mutating the Asp (to Gly) reduces activity by 2700-fold indicates an important role in catalysis, but probably not one as the nucleophile in a double-displacement reaction, as previously suggested. Consistent with direct-displacement hydrolysis, a structure of the enzyme-product complex indicates a reaction leading to inversion of configuration. A structure with DNA containing 1-azadeoxyribose models a potential oxacarbenium-ion intermediate and suggests the Asp could facilitate migration of the electrophile towards the nucleophilic water. Finally, the structures provide detailed snapshots of the HhH motif, informing how these ubiquitous metal-binding elements mediate DNA binding.     

The first vitamin B6 zinc complex, pyridoxinato-zinc acetate: A 1D coordination polymer with polar packing through strong inter-chain hydrogen bonding

The biologically important pyridoxinato(1−) ligand (anionic vitamin B₆) shows the rare phenolate-hydroxymethyl chelation plus bridging mode through the pyridine-nitrogen atom towards zinc(II) to give the one-dimensional (1D) coordination polymer {(acetato-κO)-aqua-μ-[2-methyl-3-oxy-4,5-di(hydroxymethyl)pyridine-κN:O,O′]zinc(II)}·monohydrate with polar packing of adjacent chains along the polar c axis (in space group Pc) through strong inter-chain hydrogen bonding.     

Categorical Rhythms Are Shared between Songbirds and Humans

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Ultrastructure of the developing pigment strand of rice (Oryza sativa L.) in relation to its role in solute transport

Summary The developing pigment strand of rice (Oryza sativa L.) was studied by conventional electron microscopy and also by use of thick sections post-fixed with zinc iodide and osmium (ZIO).When the rice caryopsis achieves maximum length, a suberised adcrusting wall layer is laid down over the original primary walls of the pigment strand. Concomitant with suberin deposition a proliferation of tubular endoplasmic reticulum occurs in the cytoplasm giving rise to numerous interconnected vesicles which bear ribosomes. The vesicles in the general cytoplasm retain their ribosomes while those close to the wall become smooth and contain an electron-opaque granular material which is eventually deposited to the outside of the plasmalemma. This granular material may be the precursor(s) from which suberin is polymerised. The suberised wall attains about six times the width of the original primary wall and plasmodesmata, which traverse both primary wall and suberised wall layers, become greatly elongated.Lipid bodies increase in both size and frequency during development, eventually coalescing to form a complete plug across the pigment strand and occluding the symplast of this tissue. The significance of these ultrastructural observations is discussed in relation to the previously demonstrated role of the pigment strand as a translocation pathway for water and assimilates during grain filling.Abbreviations ER endoplasmic reticulum - ZIO zinc iodide-osmium fixation     

Substantivity of zinc salts used as rinsing solutions and their effect on the inhibition of Streptococcus mutans

The antimicrobial efficacy of zinc (Zn) salts (sulfate and acetate) against Streptococcus mutans (S. mutans) present in the oral cavity was tested in this study. The substantivity of Zn salts was assessed by determining the concentration of Zn in whole, unstimulated saliva and by measuring the magnitude of suppression of salivary S. mutans, 2h after rinsing. The concentration of Zn was measured by atomic absorption spectrometry (AAS) with electrothermal atomization (ET AAS) in saliva sampled before (basal) and 24h after mouth rinsing with different concentrations of Zn (0.1%, 0.5% and 1%) administrated as sulfate and acetate. The estimation of Zn levels in samples collected 30, 60, 90 and 120 min after rinsing was carried out by AAS with flame atomization (FAAS). Immediately after rinsing, the concentration of Zn in saliva sharply increased with respect to the baseline values (0.055+/-0.017 mg/L), followed by a sustained decrease, probably due to clearance of salivary flow or swallowing during sampling. A significant reduction (>87%) in the total mean S. mutans counts was found 2h after rinsing either with sulfate or acetate solutions, as evidence of the high substantivity and effectiveness of the Zn salts tested. A statistically significant inverse relationship (p<0.001 and the Pearson correlation coefficients between -34% and -50%) was found between Zn levels and the respective pH values measured in the samples collected 60 and 120 min after rinsing, sustaining the theory of bacterial glycolysis inhibition.     

Acetylation of SUMO1 Alters Interactions with the SIMs of PML and Daxx in a Protein-Specific Manner

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Arginine utilization by Mycoplasma fermentans is not regulated by glucose metabolism: A 13C-NMR study

Abstract Electrofusion of protoplasts of two mutant strains of Hansenula polymorpha resulted in high fusion and hybrid yields when the calcium ions present in the conventional fusion medium replaced by zinc ions. The optimal fusion conditions were an alignment field of 0.4 kV cm⁻¹ strength and 2 MHz frequency for 30 s, followed by two consecutive pulses of 12 kV cm⁻¹ strength and 15 μs duration. With 0.05–0.1 mM zinc ions in the fusion medium an average clone number of 10⁴–10⁵ clones per 10⁸ input cells was reached. The presence of about 0.6 mM magnesium ions in the zinc fusion medium was essential.     

Impact of seminal and serum zinc on semen quality and hormonal status: A population-based cohort study of Russian young men

BackgroundTrace elements are important factors in human reproductive health. Among them, special attention is paid to zinc, which is an essential trace element and is necessary for the normal functioning of the male reproductive system and the process of spermatogenesis. The aim of the study was to investigate the association between seminal and serum zinc concentrations and semen quality and reproductive hormone levels in population of Russian young men.MethodsThe study population consisted of 626 young Russian men (median age 22.5 years), recruited from the general population, regardless of their fertility status. Each participant provided semen and blood sample, information about his lifestyle and ethnicity. Semen quality (sperm concentration, motility and morphology), reproductive hormone levels (testosterone, estradiol, LH, FSH and inhibin B), and serum and seminal zinc concentrations were evaluated. The semen samples were analyzed according to the WHO laboratory manual (WHO, 2010). Serum hormones were measured by enzyme immunoassay, zinc concentrations were determined using spectrophotometry and direct colorimetry without deproteinization.ResultsZinc was present in the seminal plasma in a significantly higher concentration than in the blood serum (median serum Zn concentration was 23.6 μmol/L vs seminal Zn concentration 1571.8 μmol/L). The seminal zinc concentration was positively related to the total sperm count, sperm concentration, progressive motility and normal morphology (Spearman’s test: 0.221; 0.286; 0.269; 0.183, respectively, p < 0.001), while the serum Zn concentration was negatively related to serum testosterone and estradiol levels (r = −0.249 and r = −0.096, respectively, p < 0.001−0.05). It was found that the seminal Zn content in men with normal semen quality was higher compared to men with lowered semen quality (means: 6.37 and 5.03 μmol/ejaculate, respectively, p < 0.001). Similarly, the semen volume, total sperm count, sperm concentration, progressive motility, normal morphology and the serum testosterone level in men with the seminal Zn deficiency were lower than in men with the normal seminal Zn content.ConclusionBased on the results of our population-based study, seminal Zn levels were closely associated with semen parameters in young men, so Zn deficiency may be an important risk factor for lowered semen quality. Seminal Zn determinations should be considered as a useful tool in addition to other parameters in assessing male fertility.     

Zinc,copper, selenium,and glutathione peroxidase in blood of 11-yr-old dunedin,New Zealand children

Blood was obtained from 564 11-yr-old children who had participated since birth in a multidisciplinary health and development study. Serum zinc concentration did not differ between the boys and the girls (mean±SD: 91=17 μg/100 mL,n=453). Five-6% of serum zinc values were low; although there was a weak correlation with height, none of the boys with low values were below the 10th percentile for height for this group. Serum copper concentration (112±24 μg/100 mL,n=454) was unrelated to sex, height, weight, body mass index, socioeconomic status (SES), or iron status. Blood selenium concentration (49±10 ng/mL,n=564) was lower than previously reported for Dunedin children; it was higher in children in the lower SES categories. The data represent normal values for healthy, 11-yr-old NZ children.