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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 469 records · Page 26
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Biomimetic CO oxidation below -100 °C by a nitrate-containing metal-free microporous system

CO oxidation is of importance both for inorganic and living systems. Transition and precious metals supported on various materials can oxidize CO to CO 2 . Among them, few systems, such as Au/TiO 2 , can perform CO oxidation at temperatures as low as -70 °C. Living (an)aerobic organisms perform CO oxidation with nitrate using complex enzymes under ambient temperatures representing an essential pathway for life, which enables respiration in the absence of oxygen and leads to carbonate mineral formation. Herein, we report that CO can be oxidized to CO 2 by nitrate at -140 °C within an inorganic, nonmetallic zeolitic system. The transformation of NO x and CO species in zeolite as well as the origin of this unique activity is clarified using a joint spectroscopic and computational approach.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Molecular basis of the pleiotropic effects by the antibiotic amikacin on the ribosome

Aminoglycosides are a class of antibiotics that bind to ribosomal RNA and exert pleiotropic effects on ribosome function. Amikacin, the semisynthetic derivative of kanamycin, is commonly used for treating severe infections with multidrug-resistant, aerobic Gram-negative bacteria. Amikacin carries the 4-amino-2-hydroxy butyrate (AHB) moiety at the N 1 amino group of the central 2-deoxystreptamine (2-DOS) ring, which may confer amikacin a unique ribosome inhibition profile. Here we use in vitro fast kinetics combined with X-ray crystallography and cryo-EM to dissect the mechanisms of ribosome inhibition by amikacin and the parent compound, kanamycin. Amikacin interferes with tRNA translocation, release factor-mediated peptidyl-tRNA hydrolysis, and ribosome recycling, traits attributed to the additional interactions amikacin makes with the decoding center. The binding site in the large ribosomal subunit proximal to the 3’-end of tRNA in the peptidyl (P) site lays the groundwork for rational design of amikacin derivatives with improved antibacterial properties.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

A universal metabolite repair enzyme removes a strong inhibitor of the TCA cycle

Abstract A prevalent side-reaction of succinate dehydrogenase oxidizes malate to enol-oxaloacetate (OAA), a metabolically inactive form of OAA that is a strong inhibitor of succinate dehydrogenase. We purified from cow heart mitochondria an enzyme (OAT1) with OAA tautomerase (OAT) activity that converts enol-OAA to the physiological keto-OAA form, and determined that it belongs to the highly conserved and previously uncharacterized Fumarylacetoacetate_hydrolase_domain-containing protein family. From all three domains of life, heterologously expressed proteins were shown to have strong OAT activity, and ablating the OAT1 homolog caused significant growth defects. In Escherichia coli , expression of succinate dehydrogenase was necessary for OAT1-associated growth defects to occur, and ablating OAT1 caused a significant increase in acetate and other metabolites associated with anaerobic respiration. OAT1 increased the succinate dehydrogenase reaction rate by 35% in in vitro assays with physiological concentrations of both succinate and malate. Our results suggest that OAT1 is a universal metabolite repair enzyme that is required to maximize aerobic respiration efficiency by preventing succinate dehydrogenase inhibition.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Branched-chain amino acid specialization drove diversification within Calditenuaceae ( Caldarchaeia ) and enables their cultivation

Many thermophiles that are abundant in high-temperature geothermal systems have never been cultivated and are poorly understood, including deeply branching members of the archaeal phylum Thermoproteota. Here, we describe the genome-guided cultivation of one such organism, Calditenuis ramacidaminiphagus, and show that it has evolved a heterotrophic metabolism focused on branched-chain amino acids (BCAAs). Initially, fluorescence in situ hybridization and nanoscale secondary ion mass spectrometry (FISH-nanoSIMS) showed that Cal. ramacidaminiphagus assimilated amino acids rapidly in casamino acid-amended enrichment cultures. Metagenome and metaproteome analyses showed a high abundance and expression of BCAA transporter genes, suggesting a BCAA-focused metabolism. This inference was supported by the subsequent enrichment of Cal. ramacidaminiphagus in BCAA-fed cultures, reaching 2.66×10 6 cells/mL and 48.7% of the community, whereas it was outcompeted when polar amino acids were included. Metabolic reconstruction and metaproteomics suggest that BCAAs are channeled into the mevalonate pathway for lipid biosynthesis and fuel ATP production through the TCA cycle coupled with aerobic respiration and through production of branched-chain organic acids by overflow metabolism. Ancestral state reconstructions and phylogenetic analyses of 62 Caldarchaeales genomes revealed multiple horizontal transfers of BCAA transporters to the ancestor of the genus Calditenuis. Our study highlights the crucial role of BCAAs in the early evolution and niche of this genus, and suggests a high degree of resource partitioning even within low-diversity thermophilic communities.

Biological and medical sciences↗
DOE OSTI2023

Oxygen priming induced by elevated CO 2 reduces carbon accumulation and methane emissions in coastal wetlands

Warming temperatures and elevated carbon dioxide (CO 2 ) are inextricably linked global change phenomena, but are rarely manipulated together in field experiments. As a result, ecosystem-level responses to these interacting facets of global change remain poorly understood. In 2017, we started an experiment in a coastal wetland that crosses warming and elevated CO 2 , to better understand how the interactions of these factors affect the plants, biogeochemistry, and overall survival of these ecosystems. However, contrary to our expectations, when elevated CO 2 is combined with warming, the wetland accumulated less carbon, making it more vulnerable to sea-level rise. This was due to the plants transporting more oxygen into the soil, which stimulated aerobic decomposition. At the same time, the increased supply of oxygen reduced net methane (CH 4 ) emissions from the system, even though warming alone substantially increased CH 4 emission. Together, these results demonstrate that ecosystem responses to interacting facets of global change may be mediated by plant traits that regulate the soil environment. Thus, plant responses are critical for predicting future ecosystem survival and climate feedbacks.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Lignin deconstruction by anaerobic fungi

Abstract Lignocellulose forms plant cell walls, and its three constituent polymers, cellulose, hemicellulose and lignin, represent the largest renewable organic carbon pool in the terrestrial biosphere. Insights into biological lignocellulose deconstruction inform understandings of global carbon sequestration dynamics and provide inspiration for biotechnologies seeking to address the current climate crisis by producing renewable chemicals from plant biomass. Organisms in diverse environments disassemble lignocellulose, and carbohydrate degradation processes are well defined, but biological lignin deconstruction is described only in aerobic systems. It is currently unclear whether anaerobic lignin deconstruction is impossible because of biochemical constraints or, alternatively, has not yet been measured. We applied whole cell-wall nuclear magnetic resonance, gel-permeation chromatography and transcriptome sequencing to interrogate the apparent paradox that anaerobic fungi (Neocallimastigomycetes), well-documented lignocellulose degradation specialists, are unable to modify lignin. We find that Neocallimastigomycetes anaerobically break chemical bonds in grass and hardwood lignins, and we further associate upregulated gene products with the observed lignocellulose deconstruction. These findings alter perceptions of lignin deconstruction by anaerobes and provide opportunities to advance decarbonization biotechnologies that depend on depolymerizing lignocellulose.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

A genomic perspective on fungal diversity and evolution

Originating from aquatic unicellular ancestors, over the course of ~1 billion years, the fungi have evolved to occupy nearly all aerobic environments on the planet, diversified into millions of different ‘species’ and have developed complex multicellular structures. Their relatively small, simple genomes have facilitated massive-scale sequencing and allowed us to explore genome evolution across an ancient eukaryotic kingdom. With thousands of genomes from diverse lineages now available, this Review will discuss insights into fungal biology and evolution gleaned with genomics and other multi-omics approaches. Using published genomes available through GenBank and the Joint Genome Institute’s MycoCosm platform, we generated kingdom-wide phylogenies and used them to highlight how fungal genomes have changed over time. With this phylogeny as a guide, we also discuss major evolutionary transitions that occurred across the fungal kingdom. Although progress has been made, these efforts are hampered by biases in genome representation and limited characterization of gene functions. Here, in this study, we discuss these challenges and possible future directions to address them, including initiatives to characterize conserved genes of unknown function and scale up sequencing towards 10,000 annotated fungal genomes.

Mondo, Stephen J. [USDOE Joint Genome Institute (J↗
DOE OSTI2021

A novel d-xylose isomerase from the gut of the wood feeding beetle Odontotaenius disjunctus efficiently expressed in Saccharomyces cerevisiae

Carbohydrate rich substrates such as lignocellulosic hydrolysates remain one of the primary sources of potentially renewable fuel and bulk chemicals. The pentose sugar d-xylose is often present in significant amounts along with hexoses. Saccharomyces cerevisiae can acquire the ability to metabolize d-xylose through expression of heterologous d-xylose isomerase (XI). This enzyme is notoriously difficult to express in S. cerevisiae and only fourteen XIs have been reported to be active so far. We cloned a new d-xylose isomerase derived from microorganisms in the gut of the wood-feeding beetle Odontotaenius disjunctus. Although somewhat homologous to the XI from Piromyces sp. E2, the new gene was identified as bacterial in origin and the host as a Parabacteroides sp. Expression of the new XI in S. cerevisiae resulted in faster aerobic growth than the XI from Piromyces on d-xylose media. The d-xylose isomerization rate conferred by the new XI was also 72% higher, while absolute xylitol production was identical in both strains. Interestingly, increasing concentrations of xylitol (up to 8 g L –1 ) appeared not to inhibit d-xylose consumption. The newly described XI displayed 2.6 times higher specific activity, 37% lower KM for d-xylose, and exhibited higher activity over a broader temperature range, retaining 51% of maximal activity at 30 °C compared with only 29% activity for the Piromyces XI.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Coupling flux balance analysis with reactive transport modeling through machine learning for rapid and stable simulation of microbial metabolic switching

Integrating genome-scale metabolic networks with reactive transport models (RTMs) provides a detailed description of the dynamic changes in microbial growth and metabolism. Despite promising demonstrations in the past, computational inefficiency has been pointed out as a critical issue to overcome because it requires repeated application of linear programming (LP) to obtain flux balance analysis (FBA) solutions in every time step and spatial grid. To address this challenge, we propose a new simulation method where we train and validate artificial neural networks (ANNs) using randomly sampled FBA solutions and incorporate the resulting surrogate FBA model (represented as algebraic equations) into RTMs as source/sink terms. We demonstrate the efficiency of our method via a case study of Shewanella oneidensis MR-1. During aerobic growth on lactate, S. oneidensis produces metabolic byproducts (such as pyruvate and acetate), which are subsequently consumed as alternative carbon sources when the preferred nutrients are depleted. To effectively simulate these complex dynamics, we used a cybernetic approach that models metabolic switches as the outcome of dynamic competition among multiple growth options. In both zero-dimensional batch and one-dimensional column configurations, the ANN-based surrogate models achieved substantial reduction of computational time by several orders of magnitude compared to the original LP-based FBA models. Moreover, the ANN models produced robust solutions without any special measures to prevent numerical instability. These developments significantly promote our ability to utilize genome-scale networks in complex, multi-physics, and multi-dimensional ecosystem modeling.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Critical Enzyme Reactions in Aromatic Catabolism for Microbial Lignin Conversion

The application of microbes to valorize aromatic compounds derived from the abundant plant biopolymer lignin is a rapidly developing area of research that may ultimately enable viable conversion of this recalcitrant and heterogeneous resource to valuable bio-based chemical products. Starting from the three canonical lignin building blocks, which differ in the extent of aromatic ring methoxylation, several common classes of enzymatic reaction occur in the upper pathways of aromatic catabolism to prepare aromatic compounds for assimilation into central carbon metabolism, including aromatic O-demethylation, hydroxylation and decarboxylation. These critical enzymatic steps can often be rate-limiting for efficient biological funnelling of aromatic compounds. Here we review the known enzymatic mechanisms for these reactions that are relevant for aerobic aromatic catabolism of lignin-related monomers, highlighting opportunities at the intersection of biochemistry, enzyme engineering and metabolic engineering for applications in the expanding field of microbial lignin valorization.

aromatic catabolism↗
DOE OSTI2022

Mechanically interlocked pyrene-based photocatalysts

Triplet excited-state organic chromophores present countless opportunities for applications in photocatalysis. Here we describe an approach to the engineering of the triplet excited states of aromatic chromophores, which involves incorporating pyrene into pyridinium-containing mechanically interlocked molecules (MIMs). The π-extended nature of the pyrenes enforces [π···π] stacking, affording an efficient synthesis of tetrachromophoric octacationic homo[2]catenanes. These MIMs generate triplet populations and efficient intersystem crossing on account of the formation of a mixed charge-transfer/exciplex electronic state and a nanoconfinement effect, which leads to a high level of protection of the triplet state and extends the triplet lifetimes and yields. These compounds display excellent catalytic activity in photo-oxidation, as demonstrated by the aerobic oxidation of a sulfur-mustard simulant. Furthermore this research highlights the benefits of using the mechanical bond to fine-tune the triplet photophysics of existing aromatic chromophores, providing an avenue for the development of unexplored MIM-based photosensitizers and photocatalysts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Identification of a pathway for electron uptake in Shewanella oneidensis

Extracellular electron transfer (EET) could enable electron uptake into microbial metabolism for the synthesis of complex, energy dense organic molecules from CO 2 and renewable electricity. Theoretically EET could do this with an efficiency comparable to H 2 -oxidation but without the need for a volatile intermediate and the problems it causes for scale up. However, significant gaps remain in understanding the mechanism and genetics of electron uptake. For example, studies of electron uptake in electroactive microbes have shown a role for the Mtr EET complex in the electroactive microbe Shewanella oneidensis MR-1, though there is substantial variation in the magnitude of effect deletion of these genes has depending on the terminal electron acceptor used. This speaks to the potential for previously uncharacterized and/or differentially utilized genes involved in electron uptake. To address this, we screened gene disruption mutants for 3667 genes, representing ≈99% of all nonessential genes, from the S. oneidensis whole genome knockout collection using a redox dye oxidation assay. Confirmation of electron uptake using electrochemical testing allowed us to identify five genes from S. oneidensis that are indispensable for electron uptake from a cathode. Knockout of each gene eliminates extracellular electron uptake, yet in four of the five cases produces no significant defect in electron donation to an anode. This result highlights both distinct electron uptake components and an electronic connection between aerobic and anaerobic electron transport chains that allow electrons from the reversible EET machinery to be coupled to different respiratory processes in S. oneidensis. Homologs to these genes across many different genera suggesting that electron uptake by EET coupled to respiration could be widespread. These gene discoveries provide a foundation for: studying this phenotype in exotic metal-oxidizing microbes, genetic optimization of electron uptake in S. oneidensis; and genetically engineering electron uptake into a highly tractable host like E. coli to complement recent advances in synthetic CO2 fixation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Structural and mechanistic basis for redox sensing by the cyanobacterial transcription regulator RexT

Abstract Organisms have a myriad of strategies for sensing, responding to, and combating reactive oxygen species, which are unavoidable consequences of aerobic life. In the heterocystous cyanobacterium Nostoc sp. PCC 7120, one such strategy is the use of an ArsR-SmtB transcriptional regulator RexT that senses H 2 O 2 and upregulates expression of thioredoxin to maintain cellular redox homeostasis. Different from many other members of the ArsR-SmtB family which bind metal ions, RexT has been proposed to use disulfide bond formation as a trigger to bind and release DNA. Here, we present high-resolution crystal structures of RexT in the reduced and H 2 O 2 -treated states. These structures reveal that RexT showcases the ArsR-SmtB winged-helix-turn-helix fold and forms a vicinal disulfide bond to orchestrate a response to H 2 O 2 . The importance of the disulfide-forming Cys residues was corroborated using site-directed mutagenesis, mass spectrometry, and H 2 O 2 -consumption assays. Furthermore, an entrance channel for H 2 O 2 was identified and key residues implicated in H 2 O 2 activation were pinpointed. Finally, bioinformatics analysis of the ArsR-SmtB family indicates that the vicinal disulfide “redox switch” is a unique feature of cyanobacteria in the Nostocales order, presenting an interesting case where an ArsR-SmtB protein scaffold has been evolved to showcase peroxidatic activity and facilitate redox-based regulation.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Crystal structure of the 4-hydroxybutyryl-CoA synthetase (ADP-forming) from nitrosopumilus maritimus

The 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle from ammonia-oxidizing Thaumarchaeota is currently considered the most energy-efficient aerobic carbon fixation pathway. The Nitrosopumilus maritimus 4-hydroxybutyryl-CoA synthetase (ADP-forming; Nmar_0206) represents one of several enzymes from this cycle that exhibit increased efficiency over crenarchaeal counterparts. This enzyme reduces energy requirements on the cell, reflecting thaumarchaeal success in adapting to low-nutrient environments. Here we show the structure of Nmar_0206 from Nitrosopumilus maritimus SCM1, which reveals a highly conserved interdomain linker loop between the CoA-binding and ATP-grasp domains. Phylogenetic analysis suggests the widespread prevalence of this loop and highlights both its underrepresentation within the PDB and structural importance within the (ATP-forming) acyl-CoA synthetase (ACD) superfamily. This linker is shown to have a possible influence on conserved interface interactions between domains, thereby influencing homodimer stability. These results provide a structural basis for the energy efficiency of this key enzyme in the modified 3HP/4HB cycle of Thaumarchaeota.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

PDK4-dependent hypercatabolism and lactate production of senescent cells promotes cancer malignancy

Abstract Senescent cells remain metabolically active, but their metabolic landscape and resulting implications remain underexplored. Here, we report upregulation of pyruvate dehydrogenase kinase 4 (PDK4) upon senescence, particularly in some stromal cell lines. Senescent cells display a PDK4-dependent increase in aerobic glycolysis and enhanced lactate production but maintain mitochondrial respiration and redox activity, thus adopting a special form of metabolic reprogramming. Medium from PDK4 + stromal cells promotes the malignancy of recipient cancer cells in vitro, whereas inhibition of PDK4 causes tumor regression in vivo. We find that lactate promotes reactive oxygen species production via NOX1 to drive the senescence-associated secretory phenotype, whereas PDK4 suppression reduces DNA damage severity and restrains the senescence-associated secretory phenotype. In preclinical trials, PDK4 inhibition alleviates physical dysfunction and prevents age-associated frailty. Together, our study confirms the hypercatabolic nature of senescent cells and reveals a metabolic link between cellular senescence, lactate production, and possibly, age-related pathologies, including but not limited to cancer.

Endocrinology & Metabolism↗
DOE OSTI2024

Sexual dimorphism and the multi-omic response to exercise training in rat subcutaneous white adipose tissue

Subcutaneous white adipose tissue (scWAT) is a dynamic storage and secretory organ that regulates systemic homeostasis, yet the impact of endurance exercise training (ExT) and sex on its molecular landscape is not fully established. Utilizing an integrative multi-omics approach, and leveraging data generated by the Molecular Transducers of Physical Activity Consortium (MoTrPAC), we show profound sexual dimorphism in the scWAT of sedentary rats and in the dynamic response of this tissue to ExT. Specifically, the scWAT of sedentary females displays -omic signatures related to insulin signaling and adipogenesis, whereas the scWAT of sedentary males is enriched in terms related to aerobic metabolism. These sex-specific -omic signatures are preserved or amplified with ExT. Integration of multi-omic analyses with phenotypic measures identifies molecular hubs predicted to drive sexually distinct responses to training. Overall, this study underscores the powerful impact of sex on adipose tissue biology and provides a rich resource to investigate the scWAT response to ExT.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Decoupling of redox processes from soil saturation in Arctic tundra

Permafrost thaw in warming Arctic landscapes alters hydrology and saturation-driven biogeochemical processes. Models assume that aerobic respiration occurs in drained soils while saturated soils support methanogenesis; however, saturated soils maintain redox gradients that host a range of anaerobic metabolisms. We evaluated how redox potential and redox-active solutes vary with soil moisture in the active layer of permafrost-affected acidic and non-acidic tundra hillslopes. Oxidizing conditions persisted in highly permeable organic horizons of both unsaturated tussock tundra and saturated wet sedge meadows. Redox potential decreased with depth in all soils as increasing soil bulk density restricted groundwater flow and oxygen diffusion. High concentrations of dissolved iron, phosphate, and organic carbon coincided with redox boundaries below the soil surface in acidic tundra, indicating active iron redox cycling and potential release of adsorbed phosphate during iron (oxyhydr)oxide dissolution. In non-acidic tundra, weatherable minerals affected nutrient dynamics more than redox-driven iron cycling, especially in low-lying, saturated areas where thaw reached mineral soils. The role of thaw depth and the ability of saturated soils to maintain oxidizing conditions in organic surface layers highlight the importance of soil physical properties and hydrology in predicting biogeochemical processes and greenhouse gas emissions.

54 ENVIRONMENTAL SCIENCES↗