Open Questions on the Origin of Life at Anoxic Geothermal Fields

We have recently reconstructed the ??hatcheries?? of the first cells by combining geochemical analysis with phylogenomic scrutiny of the inorganic ion requirements of universal components of modern cells (Mulkidjanian et al. Proc Natl Acad Sci U S A 109:E821?C830, 2012). These ubiquitous, and by inference primordial, proteins and functional systems show affinity to and functional requirement for K⁺, Zn²⁺, Mn²⁺, and phosphate. Thus, protocells must have evolved in habitats with a high K⁺/Na⁺ ratio and relatively high concentrations of Zn, Mn and phosphorous compounds. Geochemical reconstruction shows that the ionic composition conducive to the origin of cells could not have existed in marine settings but is compatible with emissions of vapor-dominated zones of inland geothermal systems. Under an anoxic, CO₂-dominated atmosphere, the ionic composition of pools of cool, condensed vapor at anoxic geothermal fields would resemble the internal milieu of modern cells. Such pools would be lined with porous silicate minerals mixed with metal sulfides and enriched in K⁺ ions and phosphorous compounds. Here we address some questions that have appeared in print after the publication of our anoxic geothermal field scenario. We argue that anoxic geothermal fields, which were identified as likely cradles of life by using a top-down approach and phylogenomics analysis, could provide geochemical conditions similar to those which were suggested as most conducive for the emergence of life by the chemists who pursuit the complementary bottom-up strategy.     

Iron-mediated degradation of ribosomes under oxidative stress is attenuated by manganese

Protein biosynthesis is fundamental to cellular life and requires the efficient functioning of the translational machinery. At the center of this machinery is the ribosome, a ribonucleoprotein complex that depends heavily on Mg²⁺ for structure. Recent work has indicated that other metal cations can substitute for Mg²⁺, raising questions about the role different metals may play in the maintenance of the ribosome under oxidative stress conditions. Here, we assess ribosomal integrity following oxidative stress both in vitro and in cells to elucidate details of the interactions between Fe²⁺ and the ribosome and identify Mn²⁺ as a factor capable of attenuating oxidant-induced Fe²⁺-mediated degradation of rRNA. We report that Fe²⁺ promotes degradation of all rRNA species of the yeast ribosome and that it is bound directly to RNA molecules. Furthermore, we demonstrate that Mn²⁺ competes with Fe²⁺ for rRNA-binding sites and that protection of ribosomes from Fe²⁺-mediated rRNA hydrolysis correlates with the restoration of cell viability. Our data, therefore, suggest a relationship between these two transition metals in controlling ribosome stability under oxidative stress.     

ATP:Mg2+ shapes material properties of protein-RNA condensates and their partitioning of clients

Many cellular condensates are heterotypic mixtures of proteins and RNA formed in complex environments. Magnesium ions (Mg²⁺) and ATP can impact RNA folding, and local intracellular levels of these factors can vary significantly. However, the effect of ATP:Mg²⁺ on the material properties of protein-RNA condensates is largely unknown. Here, we use an in vitro condensate model of nucleoli, made from nucleophosmin 1 (NPM1) proteins and ribosomal RNA (rRNA), to study the effect of ATP:Mg²⁺. While NPM1 dynamics remain unchanged at increasing Mg²⁺ concentrations, the internal RNA dynamics dramatically slowed until a critical point, where gel-like states appeared, suggesting the RNA component alone forms a viscoelastic network that undergoes maturation driven by weak multivalent interactions. ATP reverses this arrest and liquefies the gel-like structures. ATP:Mg²⁺ also influenced the NPM1-rRNA composition of condensates and enhanced the partitioning of two clients: an arginine-rich peptide and a small nuclear RNA. By contrast, larger ribosome partitioning shows dependence on ATP:Mg²⁺ and can become reversibly trapped around NPM1-rRNA condensates. Lastly, we show that dissipative enzymatic reactions that deplete ATP can be used to control the shape, composition, and function of condensates. Our results illustrate how intracellular environments may regulate the state and client partitioning of RNA-containing condensates.     

IDENTIFICATION AND PARTIAL CHARACTERIZATION OF PROTEASES IN LARVAL PREPARATIONS OF THE CEREAL LEAF BEETLE (Oulema melanopus,CHRYSOMELIDAE, COLEOPTERA)

We determined some biochemical properties of Oulema melanopus larval gut proteases. We found adult midgut enzyme preparations yielded results similar to whole‐larval preparations, permitting studies of the very small whole‐larval preparations. Protein preparations were analyzed using FITC–casein as a substrate. Acidic pH is optimal for proteolytic activity (range 3.0–4.0). Cysteine protease activity increased at acidic pH and in the presence of β‐mercaptoethanol. Protease activities at all pH values were maximal at 45°C. Enzyme activity in larval preparations was inhibited by addition of Fe²⁺, Ca²⁺, Mg²⁺, Zn²⁺, and K⁺ (10 mM). Fe²⁺ and Zn²⁺ significantly decreased enzyme activity at all pH values, Ca²⁺ and Mg²⁺ at pH 6.2 and Mg²⁺ at pH 4.0. Inhibitors, including pepstatin A, showed the greatest inhibition at pH 4.0; phenylmethylsulfonyl fluoride, N‐p‐tosyl‐l‐phenylalanine chloromethyl ketone at pH 6.2; and phenylmethylsulfonyl fluoride, N_α‐tosyl‐l‐lysine chloromethyl ketone hydrochloride, N‐p‐tosyl‐l‐phenylalanine chloromethyl ketone, trans‐epoxysuccinyl‐l‐leucylamido‐(4‐guanidino) butane at pH of 7.6. Inhibition assays indicated that cysteine, aspartyl (cathepsin D), serine (trypsin, chymotrypsin‐like) proteases and metalloproteases act in cereal leaf beetle digestion.     

Optimization of Culture Conditions of Brevibacterium SP. A4 for the Production of Nitrile Hydratase

Optimum culture conditions of Brevibacterium sp. A4 for production of nitrile hydratase were determined by two mathematical methods: the Hadamard method and graphic analysis of response areas. A minimal medium was optimized and the basic roles of Fe²⁺ and Mg²⁺ were clearly shown. The influence of physico-chemical factors (pH, temperature and light conditions) on the culture and on nitrile hydratase were also studied. Various results permit the production of Brevibacterium sp. A4 cells with low protease and high nitrile hydratase contents.     

Oxygen Toxicity. The Influence of Adenine-Nucleotides and Phosphate on Fe2+ Autoxidation

Fecl₂, in Na phosphate buffer autoxidizes forming active oxygen species which damage deoxyribose. Di-and triphosphate adenine-nucleotides inhibit both Fe²⁺ autoxidation and deoxyribose damage in Na phosphate buffer pH 7.4. The inhibition is related to the number of charges of the adenine-nucleotide molecule: ATP at pH 7.4 is a better inhibitor than ADP; at a pH (6.5) close to the pK's of the third and fourth charge of ADP and ATP, ADP inhibition is greatly decreased whereas ATP inhibition is slightly affected. The extent of ATP inhibition of Fe²⁺ autoxidation depends both on ATP/Mg²⁺ and ATP/Fe²⁺ ratios in the reaction mixture. Formation of a Fe²⁺ -nucleotide complex appears to be the mechanism through which ATP and ADP inhibit autoxidation and thus the generation of active oxygen species. These findings are discussed in relation to physiological and pathological fluctuations of nucleotide concentrations.     

Metal chelates in the storage and transport of neurotransmitters: interactions of metal ions with biogenic amines

Abstract— Equilibrium studies on the interaction of biogenic amines with iron (Fe²⁺ and Fe³⁺) and magnesium (Mg²⁺) were undertaken in an attempt to correlate the stabilities of metal-amine chelates and the reported granule-binding affinities of the biogenic amines. By means of potentiometric equilibrium measurements at 25°C and an ionic strength of 10 (KNO₃) the formation constants of the Fe²⁺ chelates with norepinephrine (NE) and adenosine-S-triphosphate (ATP) were determined. Possible structures were derived for the co-ordinate binding of Fe^{2 +} with NE. The interactions of Fe²⁺ and Fe²⁺-ATP with NE were investigated and the formation of Fe²⁺-NE-ATP (1:1:1) mixed ligand ternary chelate was proposed on the basis of the equilibrium data. Information obtained from chelation studies of Fe²⁺ with pyrocatechol and ethanolamine taken together with the data obtained on the Fe²⁺-NE system indicated that the binding of Fe²⁺ by NE was probably via the pyrocatechol moiety. Equilibrium constants for the binding of tyramine (TA) dopamine (DA) and NE with Mg²⁺ were also determined. The equilibrium data obtained on the Mg²⁺-amine systems indicated a correlation between the metal-amine binding affinities and the structure and amine-release (and storage) activities of the biogenic amines. A consideration of the stabilities of the Fe²⁺ and Mg²⁺ chelates together with the occurrence of these metal ions in synaptosomes suggests their possible involvement in the intra vesicular amine-binding and storage sites.     

Combined effects of waterlogging and salinity on electrochemistry, water-soluble cations and water dispersible clay in soils with various salinity levels

The combination effects of waterlogging and salinity on redox potential (Eh), pH, electric conductivity (EC), water-soluble cations (NH₄ ⁺, K⁺, Na⁺, Ca²⁺, Mg²⁺, Fe²⁺, and Mn²⁺) and water-dispersible clay (WDC) were studied in six soils collected near salt lakes in western Australia. The soils with various salinity levels were incubated under a waterlogged condition at 30 °C for 12 weeks. The Eh, pH, EC, and cations of soil solutions were monitored over the waterlogged period. The Eh values generally dropped to the lowest point within 12 days of waterlogging, then increased slightly, and reached equilibrium after 4 weeks of waterlogging. Increasing salinity levels increased soil Eh. While waterlogging increased soil pH in the first 3–4 weeks, increasing salinity level decreased soil pH during the entire waterlogging period. Waterlogging increased the EC values in the first 2 weeks, partly due to dissolution of insoluble salts. The concentrations of water-soluble NH₄ ⁺ were significantly increased with salinity level and waterlogging, and reached maximum values at week 2, and then declined to the initial level. Waterlogging and salinity increased the concentrations of water-soluble K⁺, Ca²⁺, Mg²⁺, Fe²⁺, and Mn²⁺ ions, but the magnitudes of changes were greatly affected by soil properties. Increases in water-soluble K⁺, Ca²⁺ and Mg²⁺ were attributed to increased solubility of insoluble salts, and increased competition for the adsorption sites of the soil exchange complex due to elevated concentrations of Na⁺, Fe²⁺ and Mn²⁺. Increases in water-soluble Fe²⁺ and Mn²⁺ induced by waterlogging were attributed to the dissolution of Fe and Mn oxides under reduced conditions. Waterlogging increased, but salinity decreased, the amounts of water-dispersible clay in the soils of low EC value. The higher salinity level can counteract the adverse effect of waterlogging on clay flocculation.     

Characterization of Plasma Membrane-associated Adenosine Triphosphase Activity of Oat Roots

ATPase activity of plasma membranes isolated from oat (Avena sativa L. cv. Goodfield) roots was activated by divalent cations (Mg²⁺ = Mn²⁺ > Zn²⁺ > Fe²⁺ > Ca²⁺) and further stimulated by KCl and a variety of monovalent salts, both inorganic and organic. The enzyme exhibited greater specificity for cations than anions. The presence of Mg²⁺ was necessary for KCl stimulation. Ca²⁺ was ineffective in replacing Mg²⁺ for activation of plasma membrane ATPase, but it did activate other membrane-bound ATPases. The pH optima for Mg²⁺ activation and KCl stimulation of the plasma membrane ATPase were 7.5 and 6.5, respectively.     

Functional reconstitution and characterization of the Arabidopsis Mg2+ transporter AtMRS2-10 in proteoliposomes

Magnesium (Mg²⁺) plays critical role in many physiological processes. The mechanism of Mg²⁺ transport has been well documented in bacteria; however, less is known about Mg²⁺ transporters in eukaryotes. The AtMRS2 family, which consists of 10 Arabidopsis genes, belongs to a eukaryotic subset of the CorA superfamily proteins. Proteins in this superfamily have been identified by a universally conserved GlyMetAsn motif and have been characterized as Mg²⁺ transporters. Some members of the AtMRS2 family, including AtMRS2-10, may complement bacterial mutants or yeast mutants that lack Mg²⁺ transport capabilities. Here, we report the purification and functional reconstitution of AtMRS2-10 into liposomes. AtMRS2-10, which contains an N-terminal His-tag, was expressed in Escherichia coli and solubilized with sarcosyl. The purified AtMRS2-10 protein was reconstituted into liposomes. AtMRS2-10 was inserted into liposomes in a unidirectional orientation. Direct measurement of Mg²⁺ uptake into proteoliposomes revealed that reconstituted AtMRS2-10 transported Mg²⁺ without any accessory proteins. Mutation in the GMN motif, M400 to I, inactivated Mg²⁺ uptake. The AtMRS2-10-mediated Mg²⁺ influx was blocked by Co(III)hexamine, and was independent of the external pH from 5 to 9. The activity of AtMRS2-10 was inhibited by Co²⁺ and Ni²⁺; however, it was not inhibited by Ca²⁺, Fe²⁺, or Fe³⁺. While these results indicate that AtMRS2-10 has similar properties to the bacterial CorA proteins, unlike bacterial CorA proteins, AtMRS2-10 was potently inhibited by Al³⁺. These studies demonstrate the functional capability of the AtMRS2 proteins in proteoliposomes to study structure–function relationships.     

Distribution of iron in Lake Banyoles in relation to the ecology of purple and green sulfur bacteria

The distribution of iron both in suspended sediment and in the water column has been studied during summer stratification in Lake Banyoles. In this lake, near bottom springs, a very fine material suspended sediment remains in suspension. Dissolved Fe²⁺ in interstitial water of this suspended sediment, is related to redox potential and to the bottom water inflow. In the water column, soluble iron is present in the hypolimnion of the six different basins forming Lake Banyoles. Under those conditions Fe²⁺ is partially removed by sulfide produced in the anoxic sediment. In addition, a peak of Fe²⁺ found at the density gradient level in basins C-III, C-IV and C-VI. A three compartment model on the dynamics of the processes involving iron in Lake Banyoles is proposed. The bottom springs supply oxygen to the anoxic hypolimnion affecting chemical processes of the iron cycle. The presence of phototrophic sulfur bacteria in the anoxic monimolimnion of basins C-III and C-IV can be related to the kinetics of Fe²⁺ and sulfide. In C-III sulfide concentration exceeds Fe²⁺ concentration whereas in C-IV sulfide is not detectable and iron reached values up to 60 mM. The presence of phototrophic sulfur bacteria in iron-containing environments with no detectable sulfide is explained by the ability of such microorganisms to use FeS as electron donor instead of H₂S.     

The phosphate-pyrophosphate exchange and hydrolytic reactions of the membrane-bound pyrophosphatase ofRhodospirillum rubrum: Effects of pH and divalent cations

The relation that exist between the Pi-PPi exchange reaction and pyrophosphate hydrolysis by the membrane-bound pyrophosphatase of chromatophores ofRhodospirillum rubrum was studied. The two reactions have a markedly different requirement for pH. The optimal pH for hydrolysis was 6.5 while the Pi-PPi exchange reaction was at 7.5; the pH affects mainly theK _m of Mg²⁺ or Pi for the enzyme; Mn²⁺ and Co²⁺ support the Pi-PPi exchange reaction partially (50%), but the reaction is slower than with Mg²⁺; other divalent cations like Zn²⁺ or Ca²⁺ do not support the exchange reaction. In the hydrolytic reaction, Zn²⁺, at low concentration, substitutes for Mg²⁺ as substrate, and Co²⁺ also substitutes in limited amount (50%). Other cations (Ca²⁺, Cu²⁺, Fe²⁺, etc.) do not act as substrates in complex with PPi. The Zn²⁺ at high concentrations inhibited the hydrolytic reaction, probably due to uncomplexed free Zn²⁺. In the presence of high concentration of substrate for the hydrolysis (Mg-PPi) the divalent cations are inhibitory in the following order: Zn²⁺>Mn²⁺>Ca²⁺Co²⁺>Fe²⁺>Cu²⁺>Mg²⁺. The data in this work suggest that H⁺ and divalent cations in their free form induced changes in the kinetic properties of the enzyme.     

Effects of Cd2+ and EDTA on young sugar beets (Beta vulgaris). II. Net uptake and distribution of Mg2+, Ca2+ and Fe2+/Fe3+

Levels of Mg²⁺, Ca²⁺ and Fe²⁺/Fe³⁺ were determined in roots and shoots of sugar beet seedlings (Beta vulgaris L. cv. Monohill) cultured for 5 weeks in a complete nutrient solution to which either Cd²⁺ (0, 5 or 50 μM), EDTA (0, 10 or 100 μM) or a combination of both was added. The plants subjected to the various treatments showed a variety of deficiency symptoms. Leaves of the Cd²⁺-treated plants became thin and chlorotic (Mg- and Fe-deficiency symptoms). The plants showed reduced growth and developed only a few brownish roots with short laterals (Ca-deficiency symptoms). EDTA treatment resulted in green, stunted, hard leaves and reduced growth (Ca-deficiency symptoms). The deficiency symptoms observed correspond well with the observed uptake rates and distributions of Mg²⁺, Ca²⁺ and Fe²⁺/Fe³⁺. Increases in either Cd²⁺, EDTA or a combination of both in the growth medium, were correlated with increasing Mg²⁺ levels in the roots and with decreasing Mg²⁺ levels in the shoots. Cd²⁺ alone or in combination with EDTA had little influence on Ca²⁺ levels in the shoots but decreased Ca²⁺ levels in the roots. Thus, Cd²⁺ affects Mg²⁺ and Ca²⁺ transport in opposite ways: Mg²⁺ transport to the shoots is inhibited while that of Ca²⁺ is facilitated. Treatment with EDTA alone did not affect Ca²⁺ concentrations in either the shoots or the roots. Treatment with Cd²⁺ lowered Fe²⁺ concentrations in both roots and shoots.     

Characteristics of extracellular proteases produced by Bacillus laterosporus and Flavobacterium sp. isolated from gelatinfactory effluents

Forty bacterial isolates from the effluents of a gelatin factory (Jabalpur, India) were screened for protease activity and the two most potent producers were identified as Bacillus laterosporus and a Flavobacterium sp. The enzymes of both isolates were optimal at pH 8 and 60°C, with maximum activity after 90 min. The enzyme activity of B. laterosporus was suppressed by Fe²⁺, Mg²⁺, Mn²⁺ and Zn²⁺ ions but was enhanced by Ba²⁺ and Ca²⁺. That of Flavobacterium sp. was suppressed by Mg²⁺ and Mn²⁺ ions but enhanced by Ba²⁺, Ca²⁺ and Fe²⁺. The enzyme activity of the former was strongly inhibited by KCN, whereas that of the latter was only slightly inhibited by 8-hydroxyquinoline.     

A novel model for cyanobacteria bloom formation: the critical role of anoxia and ferrous iron

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Combination of biosorption and photodegradation to remove methyl orange from aqueous solutions

In this study, metal ion‐modified biomass of waste beer yeast was prepared to improve its adsorption capacity for an anionic dye: methyl orange. The adsorption capacities of Fe³⁺‐, Mg²⁺‐, Ca²⁺,‐ and Na⁺‐modified biomass preparations for methyl orange were 90.8, 51.3, 23.0, and 20.6 mg/g, which were 30, 17, 8, and 7 times that of the unmodified biomass, respectively. Adsorption isotherm experiments showed that the Freundlich model gave better fits than the Langmuir model for methyl orange adsorption on Fe³⁺‐, Mg²⁺‐, Ca²⁺‐modified and unmodified biomass, whereas on Na⁺‐modified biomass the Langmuir model gave better fits. The sorption and desorption kinetics of methyl orange on Fe³⁺‐ and Mg²⁺‐modified biomass both fitted well to the pseudo‐second‐order kinetic models, with R≥0.998, and the desorption processes in NaOH solution (pH 12) were very fast in attaining equilibrium, i.e. within 15 min. In order to avoid secondary pollution, the eluent containing the desorbed methyl orange was treated with a photocatalyst: P25. After that, the eluent could be reused, and thus saving a large volume of eluent.     

Reduced Model Captures Mg-RNA Interaction Free Energy of Riboswitches

The stability of RNA tertiary structures depends heavily on Mg²⁺. The Mg²⁺-RNA interaction free energy that stabilizes an RNA structure can be computed experimentally through fluorescence-based assays that measure Γ₂₊, the number of excess Mg²⁺ associated with an RNA molecule. Previous explicit-solvent simulations predict that the majority of excess Mg²⁺ ions interact closely and strongly with the RNA, unlike monovalent ions such as K⁺, suggesting that an explicit treatment of Mg²⁺ is important for capturing RNA dynamics. Here we present a reduced model that accurately reproduces the thermodynamics of Mg²⁺-RNA interactions. This model is able to characterize long-timescale RNA dynamics coupled to Mg²⁺ through the explicit representation of Mg²⁺ ions. KCl is described by Debye-Hückel screening and a Manning condensation parameter, which represents condensed K⁺ and models its competition with condensed Mg²⁺. The model contains one fitted parameter, the number of condensed K⁺ ions in the absence of Mg²⁺. Values of Γ₂₊ computed from molecular dynamics simulations using the model show excellent agreement with both experimental data on the adenine riboswitch and previous explicit-solvent simulations of the SAM-I riboswitch. This agreement confirms the thermodynamic accuracy of the model via the direct relation of Γ₂₊ to the Mg²⁺-RNA interaction free energy, and provides further support for the predictions from explicit-solvent calculations. This reduced model will be useful for future studies of the interplay between Mg²⁺ and RNA dynamics.     

Effects of Metals on 3-Acetyldeoxynivalenol Production by Fusarium graminearum R2118 in Submerged Cultures

The effects of selected metals (Mg²⁺, Mn²⁺, Zn²⁺, and Fe²⁺) on 3-acetyldeoxynivalenol (3-ADN) production by Fusarium graminearum R2118 and on its mycelial growth were investigated by using a two-stage submerged-culture technique. In certain concentrations ranges, Mg²⁺ and Fe²⁺ stimulated growth but suppressed 3-ADN production; at other concentrations, Mg²⁺, Fe²⁺, and Zn²⁺ suppressed growth but stimulated 3-ADN production. In contrast, Mn²⁺ stimulated growth but totally inhibited 3-ADN production at all concentrations tested. In general, the production of 3-ADN was inversely related to the growth rate of the fungus with these metals. Mn²⁺ appears to be a crucial factor regulating the onset of 3-ADN biosynthesis.     

Anti-fibrillogenic and fibril destabilizing effects of metal ions on cystatin fibrils

Metals such as Cu²⁺, Fe³⁺, and Zn²⁺ are major contributors to the biology of a brain in stages of health, aging, and disease because of their unique effects on both protein structures (misfolding) and oxidative stress. The relationship between metal ions and neurodegenerative diseases is very complicated. Our study highlights how metal ions influence amyloid formation at low pH and on preformed amyloid fibrils. By using thioflavin T assay, ANS fluorescence, Congo red assay, circular dichroism, and microscopy to elucidate the effects of Cu²⁺, Fe³⁺, and Zn²⁺ on goat brain cystatin (GBC) aggregation at low pH. Results showed that Cu²⁺ and Fe³⁺ inhibit fibril formation of GBC by promoting amorphous aggregates. However, Zn²⁺ exclusively promotes fibril formation at low pH, leading to the formation of more ordered aggregates. Furthermore, the combined results of these complementary methods also suggested that Cu²⁺ and Fe³⁺ destabilize the β-sheet secondary structure of preformed amyloid fibrils of GBC.