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At least 811 records · Page 45

Structure of metallochaperone in complex with the cobalamin-binding domain of its target mutase provides insight into cofactor delivery

G-protein metallochaperone MeaB in bacteria [methylmalonic aciduria type A (MMAA) in humans] is responsible for facilitating the delivery of adenosylcobalamin (AdoCbl) to methylmalonyl-CoA mutase (MCM), the only AdoCbl-dependent enzyme in humans. Genetic defects in the switch III region of MMAA lead to the genetic disorder methylmalonic aciduria in which the body is unable to process certain lipids. Here, we present a crystal structure of Methylobacterium extorquens MeaB bound to a nonhydrolyzable guanosine triphosphate (GTP) analog guanosine-5'-[(β,γ)-methyleno]triphosphate (GMPPCP) with the Cbl-binding domain of its target mutase enzyme (MeMCM cbl ). This structure provides an explanation for the stimulation of the GTP hydrolyase activity of MeaB afforded by target protein binding. We find that upon MCM cbl association, one protomer of the MeaB dimer rotates ~180°, such that the inactive state of MeaB is converted to an active state in which the nucleotide substrate is now surrounded by catalytic residues. Importantly, it is the switch III region that undergoes the largest change, rearranging to make direct contacts with the terminal phosphate of GMPPCP. These structural data additionally provide insights into the molecular basis by which this metallochaperone contributes to AdoCbl delivery without directly binding the cofactor. Our data suggest a model in which GTP-bound MeaB stabilizes a conformation of MCM that is open for AdoCbl insertion, and GTP hydrolysis, as signaled by switch III residues, allows MCM to close and trap its cofactor. Substitutions of switch III residues destabilize the active state of MeaB through loss of protein:nucleotide and protein:protein interactions at the dimer interface, thus uncoupling GTP hydrolysis from AdoCbl delivery.

59 BASIC BIOLOGICAL SCIENCES↗

Endothermic physiology of extinct megatooth sharks

The evolution of the extinct megatooth shark, Otodus megalodon , and its close phylogenetic relatives remains enigmatic. A central question persists regarding the thermophysiological origins of these large predatory sharks through geologic time, including whether O. megalodon was ectothermic or endothermic (including regional endothermy), and whether its thermophysiology could help to explain the iconic shark’s gigantism and eventual demise during the Pliocene. To address these uncertainties, we present unique geochemical evidence for thermoregulation in O. megalodon from both clumped isotope paleothermometry and phosphate oxygen isotopes. Our results show that O. megalodon had an overall warmer body temperature compared with its ambient environment and other coexisting shark species, providing quantitative and experimental support for recent biophysical modeling studies that suggest endothermy was one of the key drivers for gigantism in O. megalodon and other lamniform sharks. The gigantic body size with high metabolic costs of having high body temperatures may have contributed to the vulnerability of Otodus species to extinction when compared to other sympatric sharks that survived the Pliocene epoch.

60 APPLIED LIFE SCIENCES↗

NTRC regulates CP12 to activate Calvin–Benson cycle during cold acclimation

NADPH-dependent thioredoxin reductase C (NTRC) is a chloroplast redox regulator in algae and plants. Here, we used site-specific mutation analyses of the thioredoxin domain active site of NTRC in the green alga Chlamydomonas reinhardtii to show that NTRC mediates cold tolerance in a redox-dependent manner. By means of coimmunoprecipitation and mass spectrometry, a redox- and cold-dependent binding of the Calvin–Benson Cycle Protein 12 (CP12) to NTRC was identified. NTRC was subsequently demonstrated to directly reduce CP12 of C. reinhardtii as well as that of the vascular plant Arabidopsis thaliana in vitro. As a scaffold protein, CP12 joins the Calvin–Benson cycle enzymes phosphoribulokinase (PRK) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) to form an autoinhibitory supracomplex. Using size-exclusion chromatography, NTRC from both organisms was shown to control the integrity of this complex in vitro and thereby PRK and GAPDH activities in the cold. Thus, NTRC apparently reduces CP12, hence triggering the dissociation of the PRK/CP12/GAPDH complex in the cold. Like the ntrc::aphVIII mutant, CRISPR-based cp12::emx1 mutants also exhibited a redox-dependent cold phenotype. In addition, CP12 deletion resulted in robust decreases in both PRK and GAPDH protein levels implying a protein protection effect of CP12. Both CP12 functions are critical for preparing a repertoire of enzymes for rapid activation in response to environmental changes. This provides a crucial mechanism for cold acclimation.

54 ENVIRONMENTAL SCIENCES↗

Evolving dual-trait EPSP synthase variants using a synthetic yeast selection system

The enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) functions in the shikimate pathway which is responsible for the production of aromatic amino acids and precursors of other essential secondary metabolites in all plant species. EPSPS is also the molecular target of the herbicide glyphosate. While some plant EPSPS variants have been characterized with reduced glyphosate sensitivity and have been used in biotechnology, the glyphosate insensitivity typically comes with a cost to catalytic efficiency. Thus, there exists a need to generate additional EPSPS variants that maintain both high catalytic efficiency and high glyphosate tolerance. Here, we create a synthetic yeast system to rapidly study and evolve heterologous EPSP synthases for these dual traits. Using known EPSPS variants, we first validate that our synthetic yeast system is capable of recapitulating growth characteristics observed in plants grown in varying levels of glyphosate. Next, we demonstrate that variants from mutagenesis libraries with distinct phenotypic traits can be isolated depending on the selection criteria applied. By applying strong dual-trait selection pressure, we identify a notable EPSPS mutant after just a single round of evolution that displays robust glyphosate tolerance (K i of nearly 1 mM) and improved enzymatic efficiency over the starting point (~2.5 fold). Finally, we show the crystal structure of corn EPSPS and the top resulting mutants and demonstrate that certain mutants have the potential to outperform previously reported glyphosate-resistant EPSPS mutants, such as T102I and P106S (denoted as TIPS), in whole-plant testing. Altogether, this platform helps explore the trade-off between glyphosate resistance and enzymatic efficiency.

Science & Technology - Other Topics↗

Monofluorinated acetal electrolyte for high-performance lithium metal batteries

High degree of fluorination for ether electrolytes has resulted in improved cycling stability of lithium metal batteries due to stable solid electrolyte interphase (SEI) formation and good oxidative stability. However, the sluggish ion transport and environmental concerns of high fluorination degree drive the need to develop less fluorinated structures. Here, we depart from the traditional ether backbone and introduce bis(2-fluoroethoxy)methane (F2DEM), featuring monofluorination of the acetal backbone. High coulombic efficiency and stable long-term cycling in Li||Cu half cells can be achieved with F2DEM even under fast Li metal plating conditions. The performance of F2DEM is further compared with diethoxymethane (DEM) and 2-[2-(2,2-difluoroethoxy)ethoxy]-1,1,1-trifluoroethane (F5DEE). A significantly lower overpotential is observed with F2DEM, which improves energy efficiency and enables its application in high-rate conditions. Comparative studies of F2DEM with DEM and F5DEE in anode-free lithium iron phosphate (LiFePO4) LFP pouch cells and high-loading LFP coin cells further show improved capacity retention of F2DEM electrolyte, demonstrating its practical applicability. More importantly, we also extensively investigate the underlying mechanism for the superior performance of F2DEM through various techniques, including X-ray photoelectron spectroscopy, scanning electron microscopy, cryogenic electron microscopy, focused ion beam, electrochemical impedance spectroscopy, and titration gas chromatography. Overall, F2DEM facilitates improved Li deposition morphology with reduced amount of dead Li. This enables F2DEM to show superior performance, especially under higher charging and slower discharging rate conditions.

25 ENERGY STORAGE↗

Crystal structure and catalytic mechanism of drimenol synthase, an unusual bifunctional terpene cyclase–phosphatase

Drimenol synthase fromAquimarina spongiae(AsDMS) is a highly unusual chimera that integrates two distinct, sequential isoprenoid processing activities within a single polypeptide chain. AsDMS catalyzes the class II cyclization of farnesyl diphosphate (FPP) to form drimenyl diphosphate, which then undergoes enzyme-catalyzed hydrolysis to yield drimenol, a bioactive sesquiterpene alcohol with antifungal and anticancer properties. Here, we report the X-ray crystal structures of AsDMS and its complex with a sesquiterpene thiol. The AsDMS structure exhibits a didomain architecture consisting of a terpene cyclase β domain and a haloacid dehalogenase-like phosphatase domain, with two distinct active sites located on opposite sides of the protein. Mechanistic studies show that dephosphorylation of the drimenyl diphosphate intermediate proceeds through stepwise hydrolysis such that two equivalents of inorganic phosphate rather than inorganic pyrophosphate are coproducts of the reaction sequence. When the AsDMS reaction is performed in H 2 18 O, 18 O is not incorporated into drimenol, indicating that the hydroxyl oxygen of drimenol originates from the prenyl oxygen of FPP rather than a water molecule from bulk solution. These results correct a mechanistic proposal previously advanced by another group. Surprisingly, AsDMS exhibits substrate promiscuity, catalyzing the conversion of the slowly reactive substrate mimic farnesyl-S-thiolodiphosphate into cyclic and linear sesquiterpene products. Structural and mechanistic insights gained from AsDMS illustrate the functional diversity of terpene biosynthetic enzymes and provide a foundation for engineering “designer cyclase” assemblies capable of generating a wide variety of terpenoid products.

Science & Technology - Other Topics↗

Separation and determination of ultratrace rhenium quantities in molybdenum matrix

The production of very pure molybdenum, free of Re even at ultratrace levels, is extremely important in meeting target purity specifications during the production of 99 Mo for medical applications. Here we propose two methods for separating ultratrace levels of Re from a bulk Mo matrix using either solvent extraction or extraction chromatography, combined with inductively coupled plasma quadrupole mass spectrometry (ICP-MS) detection. Re is extracted (D > 70) from solutions in sulfuric acid as a complex with tri-n-butyl phosphate. Scrubbing and washing steps result in total decontamination factors for Mo up to 1,700 for solvent extraction and 3,500 for extraction chromatography. Re is stripped into a 3 M NH 4 OH matrix and analyzed by ICP-MS. Detection (L D ) and quantification (L Q ) limits were optimized by matrix-matching to allow detection of Re in strip solutions at levels of L D = 0.1 ng Re/g-Mo and L Q = 0.3 ng Re/g-Mo in Mo powder samples. By employing these two extraction methods, excellent recoveries of Re from bulk Mo are achieved, and the L Q is improved by a factor of 5 x 10 4 .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Electrochemistry of PUREX: R is for Reduction and Ion Transfer

The PUREX (Plutonium, Uranium, Reduction, EXtraction) process is the foundation of all industrial activities that involve the recycling of plutonium and uranium from used nuclear fuel. With over 70 years of research, engineering, and operations, it can be argued that little opportunity is left for further discovery and new fundamental understandings regarding PUREX, in general, and tri-n-butyl phosphate (TBP), in particular. Through use of an advanced electroanalytical approach, molecular-level insights regarding the back-extraction of Pu(IV) by reductive separation is reported. Studies of model PUREX systems, with lanthanide ions extracted into 20 % TBP in n-dodecane, are used to demonstrate the approach. These studies reveal knowledge pertinent to mass transfer aspects of the biphasic reductive stripping reaction central to the separation of U and Pu in PUREX. Two lanthanide ions—Ce(IV) and Yb(III)—were extracted from their concentrated solutions in aqueous 3 M HNO 3 to expressly provide electrically conducting third phases to facilitate electrochemical data acquisition. To simplify the diabolically-complicated reductive separation aspects of PUREX, the controlled polarization of electrode surfaces was used to reduce Ce(IV) and Yb(III) in place of chemical reductants. Electroanalyses of the biphasic systems with Ce(IV) and Yb(III) using three-phase electrode differential pulse voltammetry demonstrate the effects of mass transfer across water-oil interfaces on the electrode potentials for the reduction to Ce(III) and Yb(II). These reductions trigger nitrate transfer out of the oil phase for Ce and proton transfer into the organic phase for Yb. This is in correlation with the transfer of the charge-neutral ion pairs Ce·3NO 3 and Yb·2NO 3 out of the oil phases. Here, the differences in ion transfer steps reflect significant variations in the equilibrium speciation of multinuclear Ce(IV) and mononuclear Yb(III) solvates of TBP in the oil phases and the loading of the organic phase.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Extraction of Neptunium, Plutonium, Americium, Zirconium, and Technetium by Di-(2-Ethylhexyl)- Iso -Butyramide (DEH i BA) at High Metal Loadings

Increased focus on carbon neutral energy has generated a resurgence of interest in nuclear power, and in particular advanced reactors which are likely to utilize high assay low enriched uranium (HALEU). This in turn could increase the economic attractiveness of recovering still partially enriched uranium from used nuclear fuel. Concomitant to development of advanced reactors, advanced reprocessing schemes should be developed which address the disadvantages to well established reprocessing schemes. The present study focuses on using di-(2-ethylhexyl)-iso-butyramide (DEHiBA) under high metal loading conditions for the reprocessing of used nuclear fuel. The elements examined in the study include the dominant transuranic actinides (Np, Pu, Am) as well as the often-problematic Tc and Zr. Further, by increasing the concentration of the extractant from the more commonly reported 1.0 M – 1.5 M, the extraction of hexavalent actinides is substantially increased, while maintaining effective rejection of tri, tetra, and pentavalent actinides, particularly in the presence of high loadings of uranium. In conclusion, the extraction of Zr by 1.5 M DEHiBA is noted to be negligible by comparison to tributyl phosphate (TBP), however the coextraction of Tc with U is observed to be nominally twice the quantity that is extracted by TBP indicating a need for effective Tc management.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

On single-crystal neutron-diffraction in DACs: quantitative structure refinement of light elements on SNAP and TOPAZ

Quantitative single crystal neutron-diffraction in diamond anvil cells has so far been limited by the neutron flux available at the various neutron sources. As a result, highly precise measurements of the exact position of light elements have not been possible preventing, for example, structural studies of hydrogen and hydrogen bonds under pressure. Here we report experiments carried out on SNAP at the Spallation Neutron Source (ORNL, TN, USA) to explore the possibility and current limits of such studies. Furthermore, we benchmarked the obtained data quality with reference experiments carried out on TOPAZ, a dedicated single-crystal instrument.We show that measuring single-crystal diffraction intensities on SNAP is possible to such a precision that we are able to resolve the hydrogen bonds in potassium dideuterium phosphate (DKDP) as well as in ice VI.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Using in situ and operando methods to characterize phase changes in charged lithium nickel cobalt aluminum oxide cathode materials

Lithium ion batteries have been extensively explored in recent decades in order to improve their electrochemical performance, address safety concerns, and reduce costs in larger-scale applications. Electrode materials are key components which govern the properties of the battery at the system level. Cathode materials are of particular importance as they are a limiting factor for achieving high energy density. Lithium nickel cobalt aluminum oxide (LiNi 0.8 Co 0.15 Al 0.05 O 2 , referred to subsequently as NCA) is one of successful cathode materials since it can deliver higher capacity than other cathode materials such as lithium cobalt oxide or lithium iron phosphate. However, structural instabilities that occur NCA during charging or at high temperatures is believed to be the primary reason for performance degradation as well as a possible safety threat. Furthermore, understanding the structural evolution that occurs in NCA is of importance to acquire fundamental insights for taking full advantage of the high capacity of NCA materials. Beyond static information, in situ and operando characterization approaches allow us to observe structural changes under external stimulus or in a working condition, providing a deeper understanding of the routes by which structure evolve. In this review, we will describe the use of both in situ and operando characterization performed with both synchrotron X-ray based techniques and advanced electron microscopy, as the combination of these techniques have been shown to be particularly effective at providing structural information at complementary length scales.

25 ENERGY STORAGE↗

Structure of amorphous materials in the NASICON system Na 1+x Ti 2 Si x P 3−x O 12

Abstract The structure of glasses in the sodium (Na) super-ionic conductor (NASICON) system Na 1 + x Ti 2 Si x P 3 − x O 12 with x = 0.8 and x = 1.0 was explored by combining neutron and high-energy x-ray diffraction with 29 Si, 31 P and 23 Na solid-state nuclear magnetic resonance (NMR) spectroscopy. The 29 Si magic angle spinning (MAS) NMR spectra reveal that the silica component remains fully polymerized in the form of Si 4 units, i.e. the silicon atoms are bound to four bridging oxygen atoms. The 31 P{ 23 Na} rotational echo adiabatic passage double resonance (REAPDOR) NMR data suggest that the 31 P MAS NMR line shape originates from four-coordinated P n units, where n = 1, 2 or 3 is the number of bridging oxygen atoms per phosphorus atom. These sites differ in their 31 P- 23 Na dipolar coupling strengths. The results support an intermediate range order scenario of a phosphosilicate mixed network-former glass in which the phosphate groups selectively attract the Na + modifier ions. Titanium takes a sub-octahedral coordination environment with a mean Ti–O coordination number of 5.17(4) for x = 0.8 and 4.86(4) for x = 1.0. A mismatch between the P–O and Si–O bond lengths of 8% is likely to inhibit the incorporation of silicon into the phosphorus sites of the NASICON crystal structure.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Accuracy of Thermodynamic Databases for Hydroxyapatite Dissolution Constant

We report that discrepancies have been noted in the solubility constant values of calcium phosphate minerals between various databases employed in widely-used aqueous speciation calculation software programs. This can cause serious errors in the calculated speciation of waters using these software programs. The aim of the present communication was to bring to light these discrepancies. Experimental determinations of the hydroxyapatite solubility product vary by as much as ten orders of magnitude as a result of experimental challenges related to the presence of impurities in the hydroxyapatite used, incongruent dissolution and the contamination of solutions with dissolved carbon dioxide. Finally, it is suggested that the value used in the database Thermo.dat is consistent with experimental data devoid of common experimental problems, while other common databases use values that lead to a vastly overestimated solubility of hydroxyapatite.

58 GEOSCIENCES↗

Metagenome-assembled genome distribution and key functionality highlight importance of aerobic metabolism in Svalbard permafrost

Permafrost underlies a large portion of the land in the Northern Hemisphere. It is proposed to be an extreme habitat and home for cold-adaptive microbial communities. Upon thaw permafrost is predicted to exacerbate increasing global temperature trend, where awakening microbes decompose millennia old carbon stocks. Yet our knowledge on composition, functional potential and variance of permafrost microbiome remains limited. In this study, we conducted a deep comparative metagenomic analysis through a 2 m permafrost core from Svalbard, Norway to determine key permafrost microbiome in this climate sensitive island ecosystem. To do so, we developed comparative metagenomics methods on metagenomic-assembled genomes (MAG). We found that community composition in Svalbard soil horizons shifted markedly with depth: the dominant phylum switched from Acidobacteria and Proteobacteria in top soils (active layer) to Actinobacteria, Bacteroidetes, Chloroflexi and Proteobacteria in permafrost layers. Key metabolic potential propagated through permafrost depths revealed aerobic respiration and soil organic matter decomposition as key metabolic traits. We also found that Svalbard MAGs were enriched in genes involved in regulation of ammonium, sulfur and phosphate. Here, we provide a new perspective on how permafrost microbiome is shaped to acquire resources in competitive and limited resource conditions of deep Svalbard soils.

59 BASIC BIOLOGICAL SCIENCES↗

Genome-wide transcriptional regulation in Saccharomyces cerevisiae in response to carbon dioxide

Sugar metabolism by Saccharomyces cerevisiae produces ample amounts of CO 2 under both aerobic and anaerobic conditions. High solubility of CO 2 in fermentation media, contributing to enjoyable sensory properties of sparkling wine and beers by S. cerevisiae, might affect yeast metabolism. To elucidate the overlooked effects of CO 2 on yeast metabolism, we examined glucose fermentation by S. cerevisiae under CO 2 as compared to N 2 and O 2 limited conditions. While both CO 2 and N 2 conditions are considered anaerobic, less glycerol and acetate but more ethanol were produced under CO 2 condition. Transcriptomic analysis revealed that significantly decreased mRNA levels of GPP1 coding for glycerol-3-phosphate phosphatase in glycerol synthesis explained the reduced glycerol production under CO 2 condition. Besides, transcriptional regulations in signal transduction, carbohydrate synthesis, heme synthesis, membrane and cell wall metabolism, and respiration were detected in response to CO 2 . Interestingly, signal transduction was uniquely regulated under CO 2 condition, where upregulated genes (STE3, MSB2, WSC3, STE12, and TEC1) in the signal sensors and transcriptional factors suggested that MAPK signaling pathway plays a critical role in CO 2 sensing and CO 2 -induced metabolisms in yeast. Furthermore, our study identifies CO 2 as an external stimulus for modulating metabolic activities in yeast and a transcriptional effector for diverse applications.

59 BASIC BIOLOGICAL SCIENCES↗

Unraveling the influence of microbial necromass on subsurface microbiomes: metabolite utilization and community dynamics

The role of microbial necromass (nonliving microbial biomass), a significant component of belowground organic carbon, in nutrient cycling and its impact on the dynamics of microbial communities in subsurface systems remains poorly understood. It is currently unclear whether necromass metabolites from various microbes are different, whether certain groups of metabolites are preferentially utilized over others, or whether different microbial species respond to various necromass metabolites. In this study, we aimed to fill these knowledge gaps by designing enrichments with necromass as the sole nutrient source for subsurface microbial communities. We used the soluble fraction of necromass from bacterial isolates belonging to Arthrobacter, Agrobacterium, and Pseudomonas genera, and our results indicate that metabolite composition of necromass varied slightly across different strains but generally included amino acids, organic acids, and nucleic acid constituents. Arthrobacter-derived necromass appeared more recalcitrant. Necromass metabolites enriched diverse microbial genera, particularly Massilia sp. responded quickly regardless of the necromass source. Despite differences in necromass utilization, microbial community composition converged rapidly over time across the three different necromass amendments. Uracil, xanthine, valine, and phosphate-containing isomers were generally depleted over time, indicating microbial assimilation for maintenance and growth. However, numerous easily assimilable metabolites were not significantly depleted, suggesting efficient necromass recycling and the potential for necromass stabilization in systems. This study highlights the dynamic interactions between microbial necromass metabolites and subsurface microbial communities, revealing both selective utilization and rapid community and necromass convergence regardless of the necromass source.

59 BASIC BIOLOGICAL SCIENCES↗

Environment-specific virocell metabolic reprogramming

Abstract Viruses impact microbial systems through killing hosts, horizontal gene transfer, and altering cellular metabolism, consequently impacting nutrient cycles. A virus-infected cell, a “virocell,” is distinct from its uninfected sister cell as the virus commandeers cellular machinery to produce viruses rather than replicate cells. Problematically, virocell responses to the nutrient-limited conditions that abound in nature are poorly understood. Here we used a systems biology approach to investigate virocell metabolic reprogramming under nutrient limitation. Using transcriptomics, proteomics, lipidomics, and endo- and exo-metabolomics, we assessed how low phosphate (low-P) conditions impacted virocells of a marine Pseudoalteromonas host when independently infected by two unrelated phages (HP1 and HS2). With the combined stresses of infection and nutrient limitation, a set of nested responses were observed. First, low-P imposed common cellular responses on all cells (virocells and uninfected cells), including activating the canonical P-stress response, and decreasing transcription, translation, and extracellular organic matter consumption. Second, low-P imposed infection-specific responses (for both virocells), including enhancing nitrogen assimilation and fatty acid degradation, and decreasing extracellular lipid relative abundance. Third, low-P suggested virocell-specific strategies. Specifically, HS2-virocells regulated gene expression by increasing transcription and ribosomal protein production, whereas HP1-virocells accumulated host proteins, decreased extracellular peptide relative abundance, and invested in broader energy and resource acquisition. These results suggest that although environmental conditions shape metabolism in common ways regardless of infection, virocell-specific strategies exist to support viral replication during nutrient limitation, and a framework now exists for identifying metabolic strategies of nutrient-limited virocells in nature.

59 BASIC BIOLOGICAL SCIENCES↗