Rationalizing the Influence of the Binding Affinity on the Activity of Phosphoserine Phosphatases.

The Sabatier principle states that catalytic activity can be maximized when the substrate binding affinity is neither too strong nor too weak. Recent studies have shown that the activity of several hydrolases is maximized at intermediate values of the binding affinity (Michaelis-Menten constant: Km ). However, it remains unclear whether this concept of artificial catalysis is applicable to enzymes in general, especially for those which have evolved under different reaction environments. Herein, we show that the activity of phosphoserine phosphatase is also enhanced at an intermediate Km value of approximately 0.5 mM. Within our dataset, the variation of Km by three orders of magnitude accounted for a roughly 18-fold variation in the activity. Owing to the high phylogenetic and physiological diversity of our dataset, our results support the importance of optimizing Km for enzymes in general. On the other hand, a 77-fold variation in the activity was attributed to other physicochemical parameters, such as the Arrhenius prefactor of kcat , and could not be explained by the Sabatier principle. Therefore, while tuning the binding affinity according to the Sabatier principle is an important consideration, the Km value is only one of many physicochemical parameters which must be optimized to maximize enzymatic activity.

Atomic-scale evidence for highly selective electrocatalytic N-N coupling on metallic MoS2.

Molybdenum sulfide (MoS2) is the most widely studied transition-metal dichalcogenide (TMDs) and phase engineering can markedly improve its electrocatalytic activity. However, the selectivity toward desired products remains poorly explored, limiting its application in complex chemical reactions. Here we report how phase engineering of MoS2 significantly improves the selectivity for nitrite reduction to nitrous oxide, a critical process in biological denitrification, using continuous-wave and pulsed electron paramagnetic resonance spectroscopy. We reveal that metallic 1T-MoS2 has a protonation site with a pKa of ∼5.5, where the proton is located ∼3.26 Šfrom redox-active Mo site. This protonation site is unique to 1T-MoS2 and induces sequential proton-electron transfer which inhibits ammonium formation while promoting nitrous oxide production, as confirmed by the pH-dependent selectivity and deuterium kinetic isotope effect. This is atomic-scale evidence of phase-dependent selectivity on MoS2, expanding the application of TMDs to selective electrocatalysis.

CO2 reduction driven by a pH gradient.

All life on Earth is built of organic molecules, so the primordial sources of reduced carbon remain a major open question in studies of the origin of life. A variant of the alkaline-hydrothermal-vent theory for life's emergence suggests that organics could have been produced by the reduction of CO2 via H2 oxidation, facilitated by geologically sustained pH gradients. The process would be an abiotic analog-and proposed evolutionary predecessor-of the Wood-Ljungdahl acetyl-CoA pathway of modern archaea and bacteria. The first energetic bottleneck of the pathway involves the endergonic reduction of CO2 with H2 to formate (HCOO-), which has proven elusive in mild abiotic settings. Here we show the reduction of CO2 with H2 at room temperature under moderate pressures (1.5 bar), driven by microfluidic pH gradients across inorganic Fe(Ni)S precipitates. Isotopic labeling with 13C confirmed formate production. Separately, deuterium (2H) labeling indicated that electron transfer to CO2 does not occur via direct hydrogenation with H2 but instead, freshly deposited Fe(Ni)S precipitates appear to facilitate electron transfer in an electrochemical-cell mechanism with two distinct half-reactions. Decreasing the pH gradient significantly, removing H2, or eliminating the precipitate yielded no detectable product. Our work demonstrates the feasibility of spatially separated yet electrically coupled geochemical reactions as drivers of otherwise endergonic processes. Beyond corroborating the ability of early-Earth alkaline hydrothermal systems to couple carbon reduction to hydrogen oxidation through biologically relevant mechanisms, these results may also be of significance for industrial and environmental applications, where other redox reactions could be facilitated using similarly mild approaches.

Multi-omics analysis on an agroecosystem reveals the significant role of organic nitrogen to increase agricultural crop yield.

Both inorganic fertilizer inputs and crop yields have increased globally, with the concurrent increase in the pollution of water bodies due to nitrogen leaching from soils. Designing agroecosystems that are environmentally friendly is urgently required. Since agroecosystems are highly complex and consist of entangled webs of interactions between plants, microbes, and soils, identifying critical components in crop production remain elusive. To understand the network structure in agroecosystems engineered by several farming methods, including environmentally friendly soil solarization, we utilized a multiomics approach on a field planted with Brassica rapa We found that the soil solarization increased plant shoot biomass irrespective of the type of fertilizer applied. Our multiomics and integrated informatics revealed complex interactions in the agroecosystem showing multiple network modules represented by plant traits heterogeneously associated with soil metabolites, minerals, and microbes. Unexpectedly, we identified soil organic nitrogen induced by soil solarization as one of the key components to increase crop yield. A germ-free plant in vitro assay and a pot experiment using arable soils confirmed that specific organic nitrogen, namely alanine and choline, directly increased plant biomass by acting as a nitrogen source and a biologically active compound. Thus, our study provides evidence at the agroecosystem level that organic nitrogen plays a key role in plant growth.

Enzyme Mimetic Active Intermediates for Nitrate Reduction in Neutral Aqueous Media.

Nitrate is a pervasive aquatic contaminant of global environmental concern. In nature, the most effective nitrate reduction reaction (NRR) is catalyzed by nitrate reductase enzymes at neutral pH, using a highly-conserved Mo center ligated mainly by oxo and thiolate groups. Mo-based NRR catalysts mostly function in organic solvents with a low water stability. Recently, an oxo-containing molybdenum sulfide nanoparticle that serves as an NRR catalyst at neutral pH was first reported. Herein, in a nanoparticle-catalyzed NRR system a pentavalent MoV (=O)S4 species, an enzyme mimetic, served as an active intermediate for the NRR. Potentiometric titration analysis revealed that a redox synergy among MoV -S, S radicals, and MoV (=O)S4 likely play a key role in stabilizing MoV (=O)S4 , showing the importance of secondary interactions in facilitating NRR. The first identification and characterization of an oxo- and thiolate-ligated Mo intermediates pave the way to the molecular design of efficient enzyme mimetic NRR catalysts in aqueous solution.

Stable Potential Windows for Long-Term Electrocatalysis by Manganese Oxides Under Acidic Conditions.

Efficient, earth-abundant, and acid-stable catalysts for the oxygen evolution reaction (OER) are missing pieces for the production of hydrogen via water electrolysis. Here, we report how the limitations on the stability of 3d-metal materials can be overcome by the spectroscopic identification of stable potential windows in which the OER can be catalyzed efficiently while simultaneously suppressing deactivation pathways. We demonstrate the benefits of this approach using gamma manganese oxide (γ-MnO2 ), which shows no signs of deactivation even after 8000 h of electrolysis at a pH of 2. This stability is vastly superior to existing acid-stable 3d-metal OER catalysts, but cannot be realized if there is a deviation as small as 50-mV from the stable potential window. A stable voltage efficiency of over 70 % in a polymer-electrolyte membrane (PEM) electrolyzer further verifies the availability of this approach and showcases how materials previously perceived to be unstable may have potential application for water electrolysis in an acidic environment.

Selective Electrocatalytic Reduction of Nitrite to Dinitrogen Based on Decoupled Proton-Electron Transfer.

The development of denitrification catalysts which can reduce nitrate and nitrite to dinitrogen is critical for sustaining the nitrogen cycle. However, regulating the selectivity has proven to be a challenge, due to the difficulty of controlling complex multielectron/proton reactions. Here we report that utilizing sequential proton-electron transfer (SPET) pathways is a viable strategy to enhance the selectivity of electrochemical reactions. The selectivity of an oxo-molybdenum sulfide electrocatalyst toward nitrite reduction to dinitrogen exhibited a volcano-type pH dependence with a maximum at pH 5. The pH-dependent formation of the intermediate species (distorted Mo(V) oxo species) identified using operando electron paramagnetic resonance (EPR) and Raman spectroscopy was in accord with a mathematical prediction that the pKa of the reaction intermediates determines the pH-dependence of the SPET-derived product. By utilizing this acute pH dependence, we achieved a Faradaic efficiency of 13.5% for nitrite reduction to dinitrogen, which is the highest value reported to date under neutral conditions.

Mechanistic Investigation of Water Oxidation Catalyzed by Uniform, Assembled MnO Nanoparticles.

The development of active water oxidation catalysts is critical to achieve high efficiency in overall water splitting. Recently, sub-10 nm-sized monodispersed partially oxidized manganese oxide nanoparticles were shown to exhibit not only superior catalytic performance for oxygen evolution, but also unique electrokinetics, as compared to their bulk counterparts. In the present work, the water-oxidizing mechanism of partially oxidized MnO nanoparticles was investigated using integrated in situ spectroscopic and electrokinetic analyses. We successfully demonstrated that, in contrast to previously reported manganese (Mn)-based catalysts, Mn(III) species are stably generated on the surface of MnO nanoparticles via a proton-coupled electron transfer pathway. Furthermore, we confirmed as to MnO nanoparticles that the one-electron oxidation step from Mn(II) to Mn(III) is no longer the rate-determining step for water oxidation and that Mn(IV)═O species are generated as reaction intermediates during catalysis.

Spontaneous and Widespread Electricity Generation in Natural Deep-Sea Hydrothermal Fields.

Deep-sea hydrothermal vents discharge abundant reductive energy into oxidative seawater. Herein, we demonstrated that in situ measurements of redox potentials on the surfaces of active hydrothermal mineral deposits were more negative than the surrounding seawater potential, driving electrical current generation. We also demonstrated that negative potentials in the surface of minerals were widespread in the hydrothermal fields, regardless of the proximity to hydrothermal fluid discharges. Lab experiments verified that the negative potential of the mineral surface was induced by a distant electron transfer from the hydrothermal fluid through the metallic and catalytic properties of minerals. These results indicate that electric current is spontaneously and widely generated in natural mineral deposits in deep-sea hydrothermal fields. Our discovery provides important insights into the microbial communities that are supported by extracellular electron transfer and the prebiotic chemical and metabolic evolution of the ocean hydrothermal systems.

Legitimate intermediates of oxygen evolution on iridium oxide revealed by in situ electrochemical evanescent wave spectroscopy.

Understanding how the four-electron oxidation of water to dioxygen proceeds in different materials is critical to the rational design of efficient catalysts towards artificial photosynthetic systems. Here, using in situ electrochemical evanescent wave spectroscopy under oxygen-evolving conditions, we report two intermediates of iridium oxide (IrOx), which is the most active and stable catalyst characterized to date in acidic medium. The observed potential dependence of the two intermediates indicated that they were associated with different surface sites, and intermediate scavenging experiments using H2O2 provided insight into their role during catalysis. Notably, an Ir(V) species with an absorption maximum at 450 nm was found to mediate the initial two-electron oxidation of water. Inhibition of the Ir(V) species by H2O2, combined with computational modeling, indicates that the accumulation and concurrent spin-state change of the Ir(V) species is a prerequisite for efficient water oxidation by IrOx electrodes.

Rate enhancement of bacterial extracellular electron transport involves bound flavin semiquinones.

Extracellular redox-active compounds, flavins and other quinones, have been hypothesized to play a major role in the delivery of electrons from cellular metabolic systems to extracellular insoluble substrates by a diffusion-based shuttling two-electron-transfer mechanism. Here we show that flavin molecules secreted by Shewanella oneidensis MR-1 enhance the ability of its outer-membrane c-type cytochromes (OM c-Cyts) to transport electrons as redox cofactors, but not free-form flavins. Whole-cell differential pulse voltammetry revealed that the redox potential of flavin was reversibly shifted more than 100 mV in a positive direction, in good agreement with increasing microbial current generation. Importantly, this flavin/OM c-Cyts interaction was found to facilitate a one-electron redox reaction via a semiquinone, resulting in a 10(3)- to 10(5)-fold faster reaction rate than that of free flavin. These results are not consistent with previously proposed redox-shuttling mechanisms but suggest that the flavin/OM c-Cyts interaction regulates the extent of extracellular electron transport coupled with intracellular metabolic activity.

Sulfur-Mediated Electron Shuttling Sustains Microbial Long-Distance Extracellular Electron Transfer with the Aid of Metallic Iron Sulfides.

In addition to serving as an energy source for microbial growth, iron sulfides are proposed to act as naturally occurring electrical wires that mediate long-distance extracellular electron transfer (EET) and bridge spatially discrete redox environments. These hypothetical EET reactions stand on the abilities of microbes to use the interfacial electrochemistry of metallic/semiconductive iron sulfides to maintain metabolisms; however, the mechanisms of these phenomena remain unexplored. To obtain insight into EET to iron sulfides, we monitored EET at the interface between Shewanella oneidensis MR-1 cells and biomineralized iron sulfides in an electrochemical cell. Respiratory current steeply increased with the concomitant formation of poorly crystalline mackinawite (FeS) minerals, indicating that S. oneidensis has the ability to exploit extracellularly formed metallic FeS for long-distance EET. Deletion of major proteins of the metal-reduction (Mtr) pathway (OmcA, MtrC, CymA, and PilD) caused only subtle effects on the EET efficiency, a finding that sharply contrasts the majority of studies that report that the Mtr pathway is indispensable for the reduction of metal oxides and electrodes. The gene expression analyses of polysulfide and thiosulfate reductase suggest the existence of a sulfur-mediated electron-shuttling mechanism by which HS(-) ions and water-soluble polysulfides (HS(n)(-), where n ≥ 2) generated in the periplasmic space deliver electrons from cellular metabolic processes to cell surface-associated FeS. The finding of this Mtr-independent pathway indicates that polysulfide reductases complement the function of outer-membrane cytochromes in EET reactions and, thus, significantly expand the number of microbial species potentially capable of long-distance EET in sulfur-rich anoxic environments.

Thermoelectricity Generation and Electron-Magnon Scattering in a Natural Chalcopyrite Mineral from a Deep-Sea Hydrothermal Vent.

Current high-performance thermoelectric materials require elaborate doping and synthesis procedures, particularly in regard to the artificial structure, and the underlying thermoelectric mechanisms are still poorly understood. Here, we report that a natural chalcopyrite mineral, Cu1+x Fe1-x S2 , obtained from a deep-sea hydrothermal vent can directly generate thermoelectricity. The resistivity displayed an excellent semiconducting character, and a large thermoelectric power and high power factor were found in the low x region. Notably, electron-magnon scattering and a large effective mass was detected in this region, thus suggesting that the strong coupling of doped carriers and antiferromagnetic spins resulted in the natural enhancement of thermoelectric properties during mineralization reactions. The present findings demonstrate the feasibility of thermoelectric energy generation and electron/hole carrier modulation with natural materials that are abundant in the Earth's crust.

Copper sulfide mineral performs non-enzymatic anaerobic ammonium oxidation through a hydrazine intermediate.

Anaerobic ammonium oxidation (anammox)-the biological process that activates ammonium with nitrite-is responsible for a significant fraction of N2 production in marine environments. Despite decades of biochemical research, however, no synthetic models capable of anammox have been identified. Here we report that a copper sulfide mineral replicates the entire biological anammox pathway catalysed by three metalloenzymes. We identified a copper-nitrosonium {CuNO}10 complex, formed by nitrite reduction, as the oxidant for ammonium oxidation that leads to heterolytic N-N bond formation from nitrite and ammonium. Similar to the biological process, N2 production was mediated by the highly reactive intermediate hydrazine, one of the most potent reductants in nature. We also found another pathway involving N-N bond heterocoupling for the formation of hybrid N2O, a potent greenhouse gas with a unique isotope composition. Our study represents a rare example of non-enzymatic anammox reaction that interconnects six redox states in the abiotic nitrogen cycle.

Gas fermentation combined with water electrolysis for production of polyhydroxyalkanoate copolymer from carbon dioxide by engineered Ralstonia eutropha.

A recycled-gas closed-circuit culture system was developed for safe autotrophic cultivation of a hydrogen-oxidizing, polyhydroxyalkanoate (PHA)-producing Ralstonia eutropha, using a non-combustible gas mixture with low-concentration of H2 supplied by water electrolysis. Automated feedback regulation of gas flow enabled input of H2, CO2, and O2 well balanced with the cellular demands, leading to constant gas composition throughout the cultivation. The engineered strain of R. eutropha produced 1.71 g/L of poly(3-hydroxybutyrate-co-12.5 mol% 3-hydroxyhexanoate) on a gas mixture of H2/CO2/O2/N2 = 4:12:7:77 vol% with a 69.2 wt% cellular content. Overexpression of can encoding cytosolic carbonic anhydrase increased the 3HHx fraction up to 19.6 mol%. The yields of biomass and PHA on input H2 were determined to be 72.9 % and 63.1 %, corresponding to 51.0 % and 44.2 % yield on electricity, respectively. The equivalent solar-to-biomass/PHA efficiencies were estimated to be 2.1-3.8 %, highlighting the high energy conversion capability of R. eutropha.

Atomically dispersed hexavalent iridium oxide from MnO2 reduction for oxygen evolution catalysis.

Hexavalent iridium (IrVI) oxide is predicted to be more active and stable than any other iridium oxide for the oxygen evolution reaction in acid; however, its experimental realization remains challenging. In this work, we report the synthesis, characterization, and application of atomically dispersed IrVI oxide (IrVI-ado) for proton exchange membrane (PEM) water electrolysis. The IrVI-ado was synthesized by oxidatively substituting the ligands of potassium hexachloroiridate(IV) (K2IrCl6) with manganese oxide (MnO2). The mass-specific activity (1.7 × 105 amperes per gram of iridium) and turnover number (1.5 × 108) exceeded those of benchmark iridium oxides, and in situ x-ray analysis during PEM operations manifested the durability of IrVI at current densities up to 2.3 amperes per square centimeter. The high activity and stability of IrVI-ado showcase its promise as an anode material for PEM electrolysis.

Extracellular electron transfer across bacterial cell membranes via a cytocompatible redox-active polymer.

A redox-active phospholipid polymer with a phospholipid-mimicking structure (2-methacryloyloxyethyl phosphorylcholine; MPC) was synthesized to construct a biocompatible electron mediator between bacteria and an electrode. In this study, a copolymer of MPC and vinylferrocene [VF; poly(MPC-co-VF)] (PMF) is synthesized. When PMF is added to cultures of the bacterial species Escherichia coli (Gram negative) and Lactobacillus plantarum (Gram positive), which have different cell wall structures, a catalytic current mediated by PMF is observed. In addition, growth curves and live/dead assays indicate that PMF does not decrease metabolic activity or cell viability. These results indicate that PMF mediates extracellular electron transfer across bacterial cell membranes without associated cytotoxicity.

Thermodynamic principle to enhance enzymatic activity using the substrate affinity.

Understanding how to tune enzymatic activity is important not only for biotechnological applications, but also to elucidate the basic principles guiding the design and optimization of biological systems in nature. So far, the Michaelis-Menten equation has provided a fundamental framework of enzymatic activity. However, there is still no concrete guideline on how the parameters should be optimized towards higher activity. Here, we demonstrate that tuning the Michaelis-Menten constant ([Formula: see text]) to the substrate concentration ([Formula: see text]) enhances enzymatic activity. This guideline ([Formula: see text]) was obtained mathematically by assuming that thermodynamically favorable reactions have higher rate constants, and that the total driving force is fixed. Due to the generality of these thermodynamic considerations, we propose [Formula: see text] as a general concept to enhance enzymatic activity. Our bioinformatic analysis reveals that the [Formula: see text] and in vivo substrate concentrations are consistent across a dataset of approximately 1000 enzymes, suggesting that even natural selection follows the principle [Formula: see text].

In situ electrosynthetic bacterial growth using electricity generated by a deep-sea hydrothermal vent.

Electroautotrophic microorganisms have attracted great attention since they exhibit a new type of primary production. Here, in situ electrochemical cultivation was conducted using the naturally occurring electromotive forces at a deep-sea hydrothermal vent. The voltage and current generation originating from the resulting microbial activity was observed for 12 days of deployment, with fluctuation in response to tidal cycles. A novel bacterium belonging to the genus Thiomicrorhabdus dominated the microbial community specifically enriched on the cathode. Metagenomic analysis provided the draft genome of the bacterium and the gene repertoire indicated that the bacterium has the potential for thio-autotrophic growth, which is a typical physiological feature of the members of the genus, while the bacterium had a unique gene cluster encoding multi-heme cytochrome c proteins responsible for extracellular electron transfer. Herein, we propose this bacterium as a new species, specifically enriched during electricity generation, as 'Candidatus Thiomicrorhabdus electrophagus'. This finding suggests the natural occurrence of electrosynthetic microbial populations using the geoelectricity in deep-sea hydrothermal environments.

Aqueous breakdown of aspartate and glutamate to n-ω-amino acids on the parent bodies of carbonaceous chondrites and asteroid Ryugu.

Amino acids in carbonaceous chondrites may have seeded the origin of life on Earth and possibly elsewhere. Recently, the return samples from a C-type asteroid Ryugu were found to contain amino acids with a similar distribution to Ivuna-type CI chondrites, suggesting the potential of amino acid abundances as molecular descriptors of parent body geochemistry. However, the chemical mechanisms responsible for the amino acid distributions remain to be elucidated particularly at low temperatures (<50°C). Here, we report that two representative proteinogenic amino acids, aspartic acid and glutamic acid, decompose to ß-alanine and γ-aminobutyric acid, respectively, under simulated geoelectrochemical conditions at 25°C. This low-temperature conversion provides a plausible explanation for the enrichment of these two n-ω-amino acids compared to their precursors in heavily aqueously altered CI chondrites and Ryugu's return samples. The results suggest that these heavily aqueously altered samples originated from the water-rich mantle of their water/rock differentiated parent planetesimals where protein α-amino acids were decomposed.