RNA structure, metal ions, and catalysis

Several new and unexpected insights into the metalloenzymology of ribozymes have been achieved in the past year. From a mechanistic point of view, the NMR and crystal structures of a small Pb(2+)-dependent ribozyme have been particularly revealing.     

EDTA enhanced heavy metal phytoextraction: metal accumulation,leaching and toxicity

Synthetic chelates such as ethylene diamine tetraacetic acid (EDTA) have been shown to enhance phytoextraction of some heavy metals from contaminated soil. In a soil column study, we examined the effect of EDTA on the uptake of Pb, Zn and Cd by Chinese cabbage (Brassica rapa), mobilization and leaching of heavy metals and the toxicity effects of EDTA additions on plants. The most effective was a single dose of 10 mmol EDTA kg^–1 soil where we detected Pb, Zn and Cd concentrations that were 104.6, 3.2 and 2.3-times higher in the aboveground plant biomass compared to the control treatments. The same EDTA addition decreased the concentration of Pb, Zn and Cd in roots of tested plants by 41, 71 and 69%, respectively compared to concentrations in the roots of control plants. In columns treated with 10 mmol kg^–1 EDTA, up to 37.9, 10.4 and 56.3% of initial total Pb, Zn and Cd in soil were leached down the soil profile, suggesting high solubility of heavy metals-EDTA complexes. EDTA treatment had a strong phytotoxic effect on the red clover (Trifolium pratense) in bioassay experiment. Moreover, the high dose EDTA additions inhibited the development of arbuscular mycorrhiza. The results of phospholipid fatty acid analyses indicated toxic effects of EDTA on soil fungi and increased environmental stress of soil microfauna.     

Toxicity,bioavailability and metal speciation

1. Environmental toxicology emphasizes the difference from traditional toxicology in which pure compounds of interest are added to purified diets, or injected into the test animals. When the objective is to study the fate and effects of trace elements in the environment, knowledge of the speciation of the elements and their physico-chemical forms is important.2. Cadmium salts such as the sulfides, carbonates or oxides, are practically insoluble in water. However, these can be converted to water-soluble salts in nature under the influence of oxygen and acids. Chronic exposure to Cd is associated with renal toxicity in humans once a critical body burden is reached.3. The solubility of As(III) oxide in water is fairly low, but high in either acid or alkali. In water, arsenic is usually in the form of the arsenate or arsenite. As(III) is systemically more poisonous than the As(V), and As(V) is reduced to the As(III) form before exerting any toxic effects. Organic arsenicals also exert their toxic effects in vivo in animals by first metabolizing to the trivalent arsenoxide form. Some methyl arsenic compounds, such as di- and trimethylarsines, occur naturally as a consequence of biological activity. The toxic effect of arsenite can be potentiated by dithiols, while As has a protective effect against the toxicity of a variety of forms of Se in several species.4. Selenium occurs in several oxidation states and many selenium analogues of organic sulfur compounds exist in nature. Selenium in selenate form occurs in alkaline soils, where it is soluble and easily available to plants. Selenite binds tightly to iron and aluminum oxides and thus is quite insoluble in soils. Hydrogen selenide is a very toxic gas at room temperature. The methylated forms of Se are much less toxic for the organism than selenite. However, the methylated Se derivatives have strong synergistic toxicity with other minerals such as arsenic.5. Aquatic organisms absorb and retain Hg in the tissues, as methylmercury, although most of the environmental Hg to which they are exposed is inorganic. The methylmercury in fish arises from the bacterial methylation of inorganic Hg. Methylmercury in the human diet is almost completely absorbed into the bloodstream. The nervous system is the principal target tissue affected by methylmercury in adult human beings, while kidney is the critical organ following the ingestion of Hg(II) salts.     

Interaction between ATP,metal ions,glycine, and several minerals

Summary The adsorption of ATP and ADP on montmorillonite, kaolinite, and A1(OH)₃ was studied as a funtion of pH and, for montmorillonite and kaolinite, as a funtion of the ionic composition of the system. The three minerals exhibit different adsorption charcteristics. Mg²⁺- and Zn²⁺-montmorillonite adsorb ATP and ADP more than Na⁺-montmorillonite, presumably because of complex formation. In kaolinite, the effect of these divalent cations is small. Pure ATP decomposes upon heating, and the rate of the decomposition is accelerated by the presence of glycine. Drying and heating glycine to 70°C under vacuum in the presence of ATP results in abiotic peptide formation with yields up to 0.25%. This peptide formation also occurs when kaolinite or montmorillonite is added to the system. The presence of kaolinite, Mg²⁺-or Zn²⁺-koalinite, or Mg²⁺-montmorillonite results in a reduction in the rate of the ATP decomposition in the abiotic peptide synthesizing system. These results suggest that one role for clays and metal ions in chemical evolution may have been the stabilization of nucleotides during prebiotic peptide synthesis.On Leave from the Hebrew University of Jerusalem, Israel     

Novel trihydroxamate-containing peptides: design, synthesis, and metal coordination

Novel trihydroxamate-containing peptides were designed to mimic desferrioxamine (Desferal(R), DFO, a naturally occurring siderophore) but possess distinct conformational restrictions and varied lipophilicity to probe structure vs. metal coordination. The synthesis was performed via fragment condensation of hydroxamate-containing oligopeptides such as Fmoc-Leu- Psi[CON(OBz)]-Phe-Ala-Pro-OH and H-Leu-Psi[CON(OBz)]-Phe-Ala-Pro-OBu(t) (Fmoc: 9-fluor enylmethoxycarbonyl; OBz: benzyl; OBu(t): tert-butyl) either in solution or on a solid support. The metal-binding properties were studied by electrospray ionization-mass spectroscopy (ESI-MS), ultraviolet (UV)-visible spectroscopy, and (1)H nuclear magnetic resonance (NMR). Similar to the dihydroxamate analogs previously explored [Biopolymers (Peptide Science), 2003, Vol. 71, pp. 489-515], the compounds with three hydroxamates arrayed at 10-atom intervals, i.e., H-[Leu-Psi[CON(OH)]-Phe-Ala-Pro](3)-OH (P1), cyclo[Leu-Psi[CON(OH)]-Phe-Ala-Pro](3) (P2), and H-[Leu-Psi(CONOH)-Phe-Ala-Pro](2)-Leu-NHOH (P7), exhibited high affinities for intramolecular coordination with Fe(III) and Ga(III). As expected, both P1 and P2 showed higher relative Fe(III)-binding affinities than the corresponding dihydroxamate-containing peptide analogs (P11 and P12). Even though both P1 and P2 did not compete with DFO in the relative metal-binding affinity in both solution and gas phases, P1, P2, and DFO exhibited similar relative binding selectivities to 11 different metal ions including Fe(III), Fe(II), Al(III), Ga(III), In(III), Zn(II), Cu(II), Co(II), Ni(II), Gd(III), and Mn(II). Compared to the other metal ions, they had higher relative binding affinities with Fe(III), Fe(II), Al(III), Ga(III), and In(III). The decreased metal-binding affinities of P1 and P2 in comparison with DFO suggested the conformational restrictions of their backbones perturb their three hydroxamate groups from optimal hexadentate orientations for metal coordination. As detected by ESI-MS, P2 was distinguished from both P1 and DFO by solvation of its Ga(III) and Fe(III) complexes (such as acetonitrile or water), thereby stabilizing the resulting complexes in the gas phase. Noteworthy, P2 led to 69% death rate in Hela cells at a concentration of 50 microM, exhibiting higher cytotoxicity than DFO in vitro despite its much lower affinity for iron. This enhanced toxicity may simply reflect the increased lipophilicity of the cyclic trihydroxamate (P2) together with the improvements in its cell penetration, and/or subsequent intracellular molecular recognition of both side chains and hydroxamate groups. The cytotoxicity was significantly suppressed by precoordination with Ga(III) or Fe(III), suggesting a mechanism of toxicity via sequestration of essential metal ions as well as the importance of curbing the metal coordination before targeting. The potential of such siderophore-mimicking peptides in oncology needs further exploration.     

A highly sensitive chelator for metal staining, bromopyridylazo-diethylaminophenol

2-(5-Bromo-2-pyridylazo)-5-diethylaminophenol has been found to be capable of staining very small amounts of metals, particularly copper, iron, lead, and zinc, in tissue. The differentiation of a target metal from interfering metals is achieved by using masking agents, polyphosphates, and potassium cyanide.     

Syntheses, structures and properties of three metal pyridinecarboxylates

Three new metal pyridinecarboxylates, namely [Co₂(pydc)₂(H₂O)₅] (1), [Mn(pydc)(H₂O)₂] (2) and [Cd₂(OH)₂(2,4-pydc)] (3), were hydrothermally synthesized. X-ray single crystal structural analysis revealed: 1 and 2 have polymeric one-dimensional chain-like structure constructed by dinuclear cobalt units and Mn-O chains, respectively; 3 has a three-dimensional layer pillared structure constructed from inorganic Cd-O layer and pydc pillars. 1 shows antiferromagnetic interaction but 2 shows alternative antiferromagnetic and ferromagnetic interactions.     

Attaching an alkali metal atom to an alkaline earth metal oxide (BeO,MgO, or CaO) yields a triatomic metal oxide with reduced ionization potential and redirected polarity

The existence of a series of neutral triatomic metal oxides MON and their corresponding cations MON ⁺ (M = Be, Mg, Ca; N = Li, Na, K) was postulated and verified theoretically using ab initio methods at the CCSD(T)/6-311+G(3df)//MP2/6-311+G(3df) level of theory. The calculations revealed that the vertical ionization potentials (IPs) of the MON radicals (calculated using the outer-valence Green’s function technique (OVGF) with the 6-311+G(3df) basis set) were ca. 2–3 eV smaller than the IPs of the corresponding MO and NO systems or that of the isolated M atom. Population analysis of the neutral triatomic MON molecules and their corresponding MO counterparts indicated that the attachment of an alkali metal atom to any oxide MO (BeO, MgO, CaO) reverses its polarity, which manifests itself as the redirection of the dipole moment vector.     

Role of ATP-bound divalent metal ion in the conformation and function of actin. Comparison of Mg-ATP, Ca-ATP, and metal ion-free ATP-actin

The fluorescence of N-acetyl-N'-(sulfo-1-naphthyl)ethylenediamine (AEDANS) covalently bound to Cys-374 of actin is used as a probe for different conformational states of G-actin according to whether Ca-ATP, Mg-ATP, or unchelated ATP is bound to the nucleotide site. Upon addition of large amounts (greater than 10(2)-fold molar excess) of EDTA to G-actin, metal ion-free ATP-G-actin is obtained with EDTA bound. Metal ion free ATP-G-actin is characterized by a higher AEDANS fluorescence than Mg-ATP-G-actin, which itself has a higher fluorescence than Ca-ATP-G-actin. Evidence for EDTA binding to G-actin is shown using difference spectrophotometry. Upon binding of EDTA, the rate of dissociation of the divalent metal ion from G-actin is increased (2-fold for Ca2+, 10-fold for Mg2+) in a range of pH from 7.0 to 8.0. A model is proposed that quantitatively accounts for the kinetic data. The affinity of ATP is weakened 10(6)-fold upon removal of the metal ion. Metal ion-free ATP-G-actin is in a partially open conformation, as indicated by the greater accessibility of -SH residues, yet it retains functional properties of polymerization and ATP hydrolysis that appear almost identical to those of Ca-ATP-actin, therefore different from those of Mg-ATP-actin. These results are discussed in terms of the role of the ATP-bound metal ion in actin structure and function.     

Degradation of sodium polyglyoxylate,a non-persistent metal sequestrant,in laboratory ecosystems

Summary Detergent builders such as zeolites, silicates and most organic polymers present concerns to some because of their environmental persistence. Sodium polyglyoxylate (SPG), on the other hand, is classified as readily biodegradable in a variety of aerobic and anaerobic biodegradation screening tests because it is extensively mineralized. Its persistence, however, is dependent on its rate of chemical hydrolysis to sodium glyoxylate, which is in turn controlled by parameters such as pH, temperature, metal ions and end capping group. The time for SPG's degradation ranges from a few hours at pH 5 to a few weeks at pH 9. Even though SPG is more persistent at alkaline pH values, it is rendered less bioavailable via precipitation/adsorption mechanisms. SPG's removal from and degradation in practically all ecosystems indicates that it will not have a significant impact on the environment with widespread use.     

Phosphorescence of octaethylchlorine, isobacteriooctaethylchlorine and their metal complexes]

The phosphorescence of dihydrooctaethylporphin (octaethylchlorin or OEC), of its complexes with magnesium, zinc, copper and palladium, and of zinc and palladium complexes of isobacteriooctaethylchlorin (5,6,7,8-tetrahydrooctaethylporphin with adjacent hydrogenated pyrrole rings or THOEP-ADJ) has been investigated. The phosphorescence spectra and phosphorescence excitation spectra as well as the ratio of fluorescence and phosphorescence yields and the triplet state lifetume have been measured. It has been shown that the singlet-triplet interval is about 4100 cm-1 for OEC complexes and about 4300 cm-1 for THOEP-ADJ complexes, and depends wealky on the nature of the metal atom forming the complex. The triplet level position of chlorophyll alpha is discussed. It is concluded that the maximum of chlorophyll alpha phosphorescence spectrum must be located at 895 nm.     

Synthesis, crystal structure and characterization of alkali metal hydroxoantimonates

Several alkali metal hydroxoantimonates, K₂[Sb(O)(OH)₅], Na[Sb(OH)₆], Cs[Sb(OH)₆] and Cs₂[Sb₂(μ-O)₂(OH)₈] were isolated from aqueous solutions and characterized by single crystal and powder X-ray diffraction studies and by FTIR and thermal analysis. Crystal structures involving [Sb(O)(OH)₅]²⁻ were never anticipated before, and this is also the first disclosure of a dinuclear antimonate [Sb₂(μ-O)₂(OH)₈]²⁻. Aqueous antimonate solutions of different pH were studied by high resolution electrospray mass spectrometry showing pH indifferent spectra and predominance of the mono and dinuclear antimonate species at pH 4-10.     

Co-occurrence of antibiotic,biocide, and heavy metal resistance genes in bacteria from metal and radionuclide contaminated soils at the Savannah River Site

Contaminants such as heavy metals may contribute to the dissemination of antimicrobial resistance (AMR) by enriching resistance gene determinants via co-selection mechanisms. In the present study, a survey was performed on soils collected from four areas at the Savannah River Site (SRS), South Carolina, USA, with varying contaminant profiles: relatively pristine (Upper Three Runs), heavy metals (Ash Basins), radionuclides (Pond B) and heavy metal and radionuclides (Tim’s Branch). Using 16S rRNA gene amplicon sequencing, we explored the structure and diversity of soil bacterial communities. Sites with legacies of metal and/or radionuclide contamination displayed significantly lower bacterial diversity compared to the reference site. Metagenomic analysis indicated that multidrug and vancomycin antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) including those associated with copper, arsenic, iron, nickel and zinc were prominent in all soils including the reference site. However, significant differences were found in the relative abundance and diversity of certain ARGs and MRGs in soils with metal/radionuclide contaminated soils compared to the reference site. Co-occurrence patterns revealed significant ARG/MRG subtypes in predominant soil taxa including Acidobacteriaceae, Bradyrhizobium, Mycobacterium, Streptomyces, Verrumicrobium, Actinomadura and Solirubacterales. Overall, the study emphasizes the potential risk of human activities on the dissemination of AMR in the environment.     

Enzyme immobilization via silochromes, modified by transition metal salts

The immobilization of pectoawamorine G 10X, pronase E and P, protease from Bac. mesentericus and rat liver microsomal fraction was performed by sylochromes modified by Ti, Zr and Hf salts. The pectinesterase, caseinolytic, esterase and hydroxylating activity of the immobilized preparations, their stability during storage, thermostability and pH optimum are determined. Of greatest interest for practical application are preparations of pectoawamorine. G 10X and pronase E and P immobilized by HfOCl2.     

细菌金属离子外排系统及金属稳态调控

铁、铜、锌、锰等金属离子是各类生物体生存和增殖所必需的微量元素,可影响生物体内蛋白酶活性、免疫反应、生理过程和抗感染机制。细菌感染过程中,宿主可通过限制或提高体内环境中金属离子的浓度来抑制细菌增殖,与此同时,细菌进化出各种转运系统以适应宿主体内金属离子水平的变化。由于不同细菌的金属离子外排系统在结构和生化特性上存在变异,它们呈现出独特的金属离子外排模式。本文根据现有文献报道及本团队研究结果,对铁、铜、锌和锰离子的细菌外排系统进行讨论和总结,旨在综述目前对细菌金属离子稳态调控机制研究进展的认识,为深入理解细菌金属稳态调控相关机制提供参考。