An organic O donor for biological hydroxylation reactions.

All biological hydroxylation reactions are thought to derive the oxygen atom from one of three inorganic oxygen donors, O2, H2O2, or H2O. Here, we have identified the organic compound prephenate as the oxygen donor for the three hydroxylation steps of the O2-independent biosynthetic pathway of ubiquinone, a widely distributed lipid coenzyme. Prephenate is an intermediate in the aromatic amino acid pathway and genetic experiments showed that it is essential for ubiquinone biosynthesis in Escherichia coli under anaerobic conditions. Metabolic labeling experiments with 18O-shikimate, a precursor of prephenate, demonstrated the incorporation of 18O atoms into ubiquinone. The role of specific iron-sulfur enzymes belonging to the widespread U32 protein family is discussed. Prephenate-dependent hydroxylation reactions represent a unique biochemical strategy for adaptation to anaerobic environments.

Zr-Based MOF-545 Metal-Organic Framework Loaded with Highly Dispersed Small Size Ni Nanoparticles for CO2 Methanation.

We report the use of Zr-based metal-organic frameworks (MOFs) MOF-545 and MOF-545(Cu) as supports to prepare catalysts with uniformly and highly dispersed Ni nanoparticles (NPs) for CO2 hydrogenation into CH4. In the first step, we studied the MOF support under catalytic conditions using operando diffuse reflectance infrared Fourier transform (DRIFT) spectroscopy, ex situ characterizations (PXRD, XPS, TEM, and EDX-element mapping), and DFT calculations. We showed that the high-temperature conditions undoubtedly confer a potential for catalytic functionality to the solids toward CH4 production, while no role of the Cu could be evidenced. The MOF was shown to be transformed into a catalytically active material, amorphized but still structured with dehydroxylated Zr-oxoclusters, in line with DFT calculations. In the second step, Ni@MOF-545 catalysts were prepared using either impregnation (IM) or double solvent (DS) methods, followed by a dry reduction (R) route under H2 to immobilize Ni NPs. The highest catalytic activity was obtained with the Ni@MOF-545 DS R catalyst (595 mmolCH4 gNi-1 h-1) with 100% CH4 selectivity and 60% CO2 conversion after ∼3 h. The higher catalytic activity of Ni@MOF-545 DS R is a result of much smaller (∼5 nm) and better dispersed Ni NPs than in the IM sample (20-40 nm), the latter exhibiting sintering. The advantages of the encapsulation of Ni NPs by the DS method and of the use of a MOF-545-based support are discussed, highlighting the interest of designing yet-unexplored Zr-based MOFs loaded with Ni NPs for CO2 hydrogenation.

Smart Electrode Surfaces by Electrolyte Immobilization for Electrocatalytic CO2 Conversion.

The activity and selectivity of molecular catalysts for the electrochemical CO2 reduction reaction (CO2RR) are influenced by the induced electric field at the electrode/electrolyte interface. We present here a novel electrolyte immobilization method to control the electric field at this interface by positively charging the electrode surface with an imidazolium cation organic layer, which significantly favors CO2 conversion to formate, suppresses hydrogen evolution reaction, and diminishes the operating cell voltage. Those results are well supported by our previous DFT calculations studying the mechanistic role of imidazolium cations in solution for CO2 reduction to formate catalyzed by a model molecular catalyst. This smart electrode surface concept based on covalent grafting of imidazolium on a carbon electrode is successfully scaled up for operating at industrially relevant conditions (100 mA cm-2) on an imidazolium-modified carbon-based gas diffusion electrode using a flow cell configuration, where the CO2 conversion to formate process takes place in acidic aqueous solution to avoid carbonate formation and is catalyzed by a model molecular Rh complex in solution. The formate production rate reaches a maximum of 4.6 gHCOO- m-2 min-1 after accumulating a total of 9000 C of charge circulated on the same electrode. Constant formate production and no significant microscopic changes on the imidazolium-modified cathode in consecutive long-term CO2 electrolysis confirmed the high stability of the imidazolium organic layer under operating conditions for CO2RR.

Activation of Coq6p, a FAD Monooxygenase Involved in Coenzyme Q Biosynthesis, by Adrenodoxin Reductase/Ferredoxin.

Adrenodoxin reductase (AdxR) plays a pivotal role in electron transfer, shuttling electrons between NADPH and iron/sulfur adrenodoxin proteins in mitochondria. This electron transport system is essential for P450 enzymes involved in various endogenous biomolecules biosynthesis. Here, we present an in-depth examination of the kinetics governing the reduction of human AdxR by NADH or NADPH. Our results highlight the efficiency of human AdxR when utilizing NADPH as a flavin reducing agent. Nevertheless, akin to related flavoenzymes such as cytochrome P450 reductase, we observe that low NADPH concentrations hinder flavin reduction due to intricate equilibrium reactions between the enzyme and its substrate/product. Remarkably, the presence of MgCl2 suppresses this complex kinetic behavior by decreasing NADPH binding to oxidized AdxR, effectively transforming AdxR into a classical Michaelis-Menten enzyme. We propose that the addition of MgCl2 may be adapted for studying the reductive half-reactions of other flavoenzymes with NADPH. Furthermore, in vitro experiments provide evidence that the reduction of the yeast flavin monooxygenase Coq6p relies on an electron transfer chain comprising NADPH-AdxR-Yah1p-Coq6p, where Yah1p shuttles electrons between AdxR and Coq6p. This discovery explains the previous in vivo observation that Yah1p and the AdxR homolog, Arh1p, are required for the biosynthesis of coenzyme Q in yeast.

Structure-based insights into the mechanism of [4Fe-4S]-dependent sulfur insertase LarE.

Several essential cellular metabolites, such as enzyme cofactors, contain sulfur atoms and their biosynthesis requires specific thiolation enzymes. LarE is an ATP-dependent sulfur insertase, which catalyzes the sequential conversion of the two carboxylate groups of the precursor of the lactate racemase cofactor into thiocarboxylates. Two types of LarE enzymes are known, one that uses a catalytic cysteine as a sacrificial sulfur donor, and the other one that uses a [4Fe-4S] cluster as a cofactor. Only the crystal structure of LarE from Lactobacillus plantarum (LpLarE) from the first class has been solved. We report here the crystal structure of LarE from Methanococcus maripaludis (MmLarE), belonging to the second class, in the cluster-free (apo-) and cluster-bound (holo-) forms. The structure of holo-MmLarE shows that the [4Fe-4S] cluster is chelated by three cysteines only, leaving an open coordination site on one Fe atom. Moreover, the fourth nonprotein-bonded iron atom was able to bind an anionic ligand such as a phosphate group or a chloride ion. Together with the spectroscopic analysis of holo-MmLarE and the previously reported biochemical investigations of holo-LarE from Thermotoga maritima, these crystal structures support the hypothesis of a reaction mechanism, in which the [4Fe-4S] cluster binds a hydrogenosulfide ligand in place of the chloride anion, thus generating a [4Fe-5S] intermediate, and transfers it to the substrate, as in the case of [4Fe-4S]-dependent tRNA thiolation enzymes.

Silver and Copper Nitride Cooperate for CO Electroreduction to Propanol.

The need of carbon sources for the chemical industry, alternative to fossil sources, has pointed to CO2 as a possible feedstock. While CO2 electroreduction (CO2 R) allows production of interesting organic compounds, it suffers from large carbon losses, mainly due to carbonate formation. This is why, quite recently, tandem CO2 R, a two-step process, with first CO2 R to CO using a solid oxide electrolysis cell followed by CO electroreduction (COR), has been considered, since no carbon is lost as carbonate in either step. Here we report a novel copper-based catalyst, silver-doped copper nitride, with record selectivity for formation of propanol (Faradaic efficiency: 45 %), an industrially relevant compound, from CO electroreduction in gas-fed flow cells. Selective propanol formation occurs at metallic copper atoms derived from copper nitride and is promoted by silver doping as shown experimentally and computationally. In addition, the selectivity for C2+ liquid products (Faradaic efficiency: 80 %) is among the highest reported so far. These findings open new perspectives regarding the design of catalysts for production of C3 compounds from CO2 .

Light-Driven Hydrogen Evolution Reaction Catalyzed by a Molybdenum-Copper Artificial Hydrogenase.

Orange protein (Orp) is a small bacterial metalloprotein of unknown function that harbors a unique molybdenum/copper (Mo/Cu) heterometallic cluster, [S2MoS2CuS2MoS2]3-. In this paper, the performance of Orp as a catalyst for the photocatalytic reduction of protons into H2 has been investigated under visible light irradiation. We report the complete biochemical and spectroscopic characterization of holo-Orp containing the [S2MoS2CuS2MoS2]3- cluster, with docking and molecular dynamics simulations suggesting a positively charged Arg, Lys-containing pocket as the binding site. Holo-Orp exhibits excellent photocatalytic activity, in the presence of ascorbate as the sacrificial electron donor and [Ru(bpy)3]Cl2 as the photosensitizer, for hydrogen evolution with a maximum turnover number of 890 after 4 h irradiation. Density functional theory (DFT) calculations were used to propose a consistent reaction mechanism in which the terminal sulfur atoms are playing a key role in promoting H2 formation. A series of dinuclear [S2MS2M'S2MS2](4n)- clusters, with M = MoVI, WVI and M'(n+) = CuI, FeI, NiI, CoI, ZnII, CdII were assembled in Orp, leading to different M/M'-Orp versions which are shown to display catalytic activity, with the Mo/Fe-Orp catalyst giving a remarkable turnover number (TON) of 1150 after 2.5 h reaction and an initial turnover frequency (TOF°) of 800 h-1 establishing a record among previously reported artificial hydrogenases.

The thiolation of uridine 34 in tRNA, which controls protein translation, depends on a [4Fe-4S] cluster in the archaeum Methanococcus maripaludis.

Thiolation of uridine 34 in the anticodon loop of several tRNAs is conserved in the three domains of life and guarantees fidelity of protein translation. U34-tRNA thiolation is catalyzed by a complex of two proteins in the eukaryotic cytosol (named Ctu1/Ctu2 in humans), but by a single NcsA enzyme in archaea. We report here spectroscopic and biochemical experiments showing that NcsA from Methanococcus maripaludis (MmNcsA) is a dimer that binds a [4Fe-4S] cluster, which is required for catalysis. Moreover, the crystal structure of MmNcsA at 2.8 Å resolution shows that the [4Fe-4S] cluster is coordinated by three conserved cysteines only, in each monomer. Extra electron density on the fourth nonprotein-bonded iron most likely locates the binding site for a hydrogenosulfide ligand, in agreement with the [4Fe-4S] cluster being used to bind and activate the sulfur atom of the sulfur donor. Comparison of the crystal structure of MmNcsA with the AlphaFold model of the human Ctu1/Ctu2 complex shows a very close superposition of the catalytic site residues, including the cysteines that coordinate the [4Fe-4S] cluster in MmNcsA. We thus propose that the same mechanism for U34-tRNA thiolation, mediated by a [4Fe-4S]-dependent enzyme, operates in archaea and eukaryotes.

Shigella IpaA mediates actin bundling through diffusible vinculin oligomers with activation imprint.

Upon activation, vinculin reinforces cytoskeletal anchorage during cell adhesion. Activating ligands classically disrupt intramolecular interactions between the vinculin head and tail domains that bind to actin filaments. Here, we show that Shigella IpaA triggers major allosteric changes in the head domain, leading to vinculin homo-oligomerization. Through the cooperative binding of its three vinculin-binding sites (VBSs), IpaA induces a striking reorientation of the D1 and D2 head subdomains associated with vinculin oligomerization. IpaA thus acts as a catalyst producing vinculin clusters that bundle actin at a distance from the activation site and trigger the formation of highly stable adhesions resisting the action of actin relaxing drugs. Unlike canonical activation, vinculin homo-oligomers induced by IpaA appear to keep a persistent imprint of the activated state in addition to their bundling activity, accounting for stable cell adhesion independent of force transduction and relevant to bacterial invasion.

Oxygen-induced chromophore degradation in the photoswitchable red fluorescent protein rsCherry.

Reversibly switchable monomeric Cherry (rsCherry) is a photoswitchable variant of the red fluorescent protein mCherry. We report that this protein gradually and irreversibly loses its red fluorescence in the dark over a period of months at 4 °C and a few days at 37 °C. We also find that its ancestor, mCherry, undergoes a similar fluorescence loss but at a slower rate. X-ray crystallography and mass spectrometry reveal that this is caused by the cleavage of the p-hydroxyphenyl ring from the chromophore and the formation of two novel types of cyclic structures at the remaining chromophore moiety. Overall, our work sheds light on a new process occurring within fluorescent proteins, further adding to the chemical diversity and versatility of these molecules.

Identification of 2-Methylthio-methylenethio-N6 -(cis-4-hydroxyisopentenyl)adenosine (msms2 io6 A37 ) as a Novel Modification at Adenosine 37 of tRNAs from Salmonella typhimurium.

Post-transcriptional modifications of tRNA nucleotide are important determinants in folding, structure and function. We have successfully identified and characterized a new modified base named 2-methylthio-methylenethio-N6 -(cis-4-hydroxyisopentenyl)adenosine, which is present at position 37 in some tRNAs. We also showed that this new modified adenosine is derived from the known 2-methylthio-methylenethio-N6 -(isopentenyl)adenosine nucleoside by a catalytic cycle of the tRNA-diiron monooxygenase, MiaE, present in Salmonella typhimurium.

A subclass of archaeal U8-tRNA sulfurases requires a [4Fe-4S] cluster for catalysis.

Sulfuration of uridine 8, in bacterial and archaeal tRNAs, is catalyzed by enzymes formerly known as ThiI, but renamed here TtuI. Two different classes of TtuI proteins, which possess a PP-loop-containing pyrophosphatase domain that includes a conserved cysteine important for catalysis, have been identified. The first class, as exemplified by the prototypic Escherichia coli enzyme, possesses an additional C-terminal rhodanese domain harboring a second cysteine, which serves to form a catalytic persulfide. Among the second class of TtuI proteins that do not possess the rhodanese domain, some archaeal proteins display a conserved CXXC + C motif. We report here spectroscopic and enzymatic studies showing that TtuI from Methanococcus maripaludis and Pyrococcus furiosus can assemble a [4Fe-4S] cluster that is essential for tRNA sulfuration activity. Moreover, structural modeling studies, together with previously reported mutagenesis experiments of M. maripaludis TtuI, indicate that the [4Fe-4S] cluster is coordinated by the three cysteines of the CXXC + C motif. Altogether, our results raise a novel mechanism for U8-tRNA sulfuration, in which the cluster is proposed to catalyze the transfer of sulfur atoms to the activated tRNA substrate.

Electrocatalytic Conversion of CO2 to Formate at Low Overpotential by Electrolyte Engineering in Model Molecular Catalysis.

An electrolyte engineering strategy was developed for CO2 reduction into formate with a model molecular catalyst, [Rh(bpy)(Cp*)Cl]Cl, by modifying the solvent (organic or aqueous), the proton source (H2 O or acetic acid), and the electrode/solution interface with imidazolium- and pyrrolidinium-based ionic liquids (ILs). Experimental and theoretical density functional theory investigations suggested that π+ -π interactions between the imidazolium-based IL cation and the reduced bipyridine ligand of the catalyst improved the efficiency of the CO2 reduction reaction (CO2 RR) by lowering the overpotential, while granting partial suppression of the hydrogen evolution reaction. This allowed tuning the selectivity towards formate, reaching for this catalyst an unprecedented faradaic efficiency (FEHCOO -) ≥90 % and energy efficiency of 66 % in acetonitrile solution. For the first time, relevant CO2 conversion to formic acid/formate was reached at low overpotential (0.28 V) using a homogeneous catalyst in acidic aqueous solution (pH=3.8). These results open up a new strategy based on electrolyte engineering for enhancing carbon balance in CO2 RR.

CO2 Electroreduction in Water with a Heterogenized C-Substituted Nickel Cyclam Catalyst.

Molecular catalysis for selective CO2 electroreduction into CO can be achieved with a variety of metal complexes. Their immobilization on cathodes is required for their practical implementation in electrolytic cells and can benefit from the advantages of a solid material such as easy separation of products and catalysts, efficient electron transfer to the catalyst, and high stability. However, this approach remains insufficiently explored up to now. Here, using an appropriate and original modification of the cyclam ligand, we report a novel [Ni(cyclam)]2+ complex which can be immobilized on carbon nanotubes. This material, once deposited on a gas diffusion layer, provides a novel electrode which is remarkably selective for CO2 electroreduction to CO, not only in organic solvents but also, more remarkably, in water, with faradic efficiencies for CO larger than 90% and current densities of 5-10 mA cm-2 during controlled potential electrolysis in H-cells.

Formate Dehydrogenase Mimics as Catalysts for Carbon Dioxide Reduction.

Formate dehydrogenases (FDH) reversibly catalyze the interconversion of CO2 to formate. They belong to the family of molybdenum and tungsten-dependent oxidoreductases. For several decades, scientists have been synthesizing structural and functional model complexes inspired by these enzymes. These studies not only allow for finding certain efficient catalysts but also in some cases to better understand the functioning of the enzymes. However, FDH models for catalytic CO2 reduction are less studied compared to the oxygen atom transfer (OAT) reaction. Herein, we present recent results of structural and functional models of FDH.

Electrocatalytic metal hydride generation using CPET mediators.

Transition metal hydrides (M-H) are ubiquitous intermediates in a wide range of enzymatic processes and catalytic reactions, playing a central role in H+/H2 interconversion1, the reduction of CO2 to formic acid (HCOOH)2 and in hydrogenation reactions. The facile formation of M-H is a critical challenge to address to further improve the energy efficiency of these reactions. Specifically, the easy electrochemical generation of M-H using mild proton sources is key to enable high selectivity versus competitive CO and H2 formation in the CO2 electroreduction to HCOOH, the highest value-added CO2 reduction product3. Here we introduce a strategy for electrocatalytic M-H generation using concerted proton-electron transfer (CPET) mediators. As a proof of principle, the combination of a series of CPET mediators with the CO2 electroreduction catalyst [MnI(bpy)(CO)3Br] (bpy = 2,2'-bipyridine) was investigated, probing the reversal of the product selectivity from CO to HCOOH to evaluate the efficiency of the manganese hydride (Mn-H) generation step. We demonstrate the formation of the Mn-H species by in situ spectroscopic techniques and determine the thermodynamic boundary conditions for this mechanism to occur. A synthetic iron-sulfur cluster is identified as the best CPET mediator for the system, enabling the preparation of a benchmark catalytic system for HCOOH generation.

Heterogenised Molecular Catalysts for Sustainable Electrochemical CO2 Reduction.

There has been a rapid rise in interest regarding the advantages of support materials to protect and immobilise molecular catalysts for the carbon dioxide reduction reaction (CO2 RR) in order to overcome the weaknesses of many well-known catalysts in terms of their stability and selectivity. In this Review, the state of the art of different catalyst-support systems for the CO2 RR is discussed with the intention of leading towards standard benchmarking for comparison of such systems across the most relevant supports and immobilisation strategies, taking into account these multiple pertinent metrics, and also enabling clearer consideration of the necessary steps for further progress. The most promising support systems are described, along with a final note on the need for developing more advanced experimental and computational techniques to aid the rational design principles that are prerequisite to prospective industrial upscaling.

Selective Ethylene Production from CO2 and CO Reduction via Engineering Membrane Electrode Assembly with Porous Dendritic Copper Oxide.

Gas-fed zero-gap electrolyzers have recently emerged as attractive systems for limiting ohmic losses and costs associated with electrolytes and for optimizing energy efficiencies. Here, we report that using a dendritic Cu oxide (D-CuO) material deposited on a gas diffusion layer as the cathode of a gas-fed zero-gap membrane electrode assembly (MEA) system results in a very selective conversion of CO to ethylene. More specifically, CO reduction yielded ethylene with an FE up to 68% at 100-125 mA·cm-2 with H2 as the only other gaseous product and the electrolysis could be carried out for several hours with good stability. Ethylene was also the major product during CO2 electrolysis (FE = 41%) at 125-150 mA·cm-2, reflecting the high selectivity of D-CuO for ethylene production. Such systems are relevant for tandem CO2 electroreduction processes, allowing energy efficiencies above 30%.

Molecular Inhibition for Selective CO2 Conversion.

Electrochemical CO2 reduction presents a sustainable route to the production of chemicals and fuels. Achieving a narrow product distribution with heterogeneous Cu catalysts is challenging and conventional material modifications offer limited control over selectivity. Here, we show that surface-immobilised molecular species can act as inhibitors for specific carbon products to provide rational control over product distributions. Combined experimental and computational results showed that anchoring of a thiol-functionalised pyridine on Cu destabilises a surface-bound reaction intermediate to energetically block a CO-producing pathway, thereby favouring formate production. The nitrogen atom was shown to be essential to the inhibition mechanism. The ability of molecules to control selectivity through inhibition of specific reaction pathways offers a unique approach to rationally modify heterogeneous catalysts.

Dihydrouridine in the Transcriptome: New Life for This Ancient RNA Chemical Modification.

Until recently, post-transcriptional modifications of RNA were largely restricted to noncoding RNA species. However, this belief seems to have quickly dissipated with the growing number of new modifications found in mRNA that were originally thought to be primarily tRNA-specific, such as dihydrouridine. Recently, transcriptomic profiling, metabolic labeling, and proteomics have identified unexpected dihydrouridylation of mRNAs, greatly expanding the catalog of novel mRNA modifications. These data also implicated dihydrouridylation in meiotic chromosome segregation, protein translation rates, and cell proliferation. Dihydrouridylation of tRNAs and mRNAs are introduced by flavin-dependent dihydrouridine synthases. In this review, we will briefly outline the current knowledge on the distribution of dihydrouridines in the transcriptome, their chemical labeling, and highlight structural and mechanistic aspects regarding the dihydrouridine synthases enzyme family. A special emphasis on important research directions to be addressed will also be discussed. This new entry of dihydrouridine into mRNA modifications has definitely added a new layer of information that controls protein synthesis.