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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Converting Second‐Order Saddle Points to Transition States: New Principles for the Design of 4π Photoswitches

Abstract Molecular photoswitches have demonstrated potential for storing solar energy at the molecular level, with power densities comparable to commercial batteries and hydroelectric energy storage. However, development of efficient photoswitches is hindered by limitations in cyclability and optical properties of existing materials. We here demonstrate that certain limitations in photoswitches based on electrocyclizations stem from the issue of controlling competition between Woodward‐Hoffmann allowed and forbidden pathways. Our approach moves beyond the traditional view of activation barriers and reveals that second‐order saddle points are crucial in dictating the competition between disrotatory and conrotatory pathways. These insights suggest new opportunities to manipulate the competition between these pathways through geometric constraints, fundamentally altering the connectivity of the potential energy surface. Our study also emphasizes the necessity of multi‐reference methods and the need to conduct higher‐dimensional explorations for competing pathways beyond photoswitch design.

Chemistry↗
DOE OSTI2024

Ru/MgO catalyst with dual Ru structure sites for efficient CO production from CO 2 hydrogenation

The development and comprehension of supported metal catalysts for CO 2 hydrogenation is of paramount importance in mitigating the net CO 2 emissions. Supported Ru catalysts have been widely recognized in facilitating CO 2 methanation, on which recent findings suggest that the CO 2 hydrogenation process can be manipulated to favor the reverse water–gas shift (RWGS) pathway by precisely adjusting the size of Ru particles. However, the size-dependent impact of Ru remains a topic of lively debate. In this work, Ru/MgO catalysts with Ru in the form of single atoms (Ru 1 ) and few-atom cluster (Ru FAC ) structures were prepared for CO 2 hydrogenation. The 1.0Ru/MgO catalyst (with 1 wt.% of Ru), featuring a mixture of Ru 1 and Ru FAC with a size of 0.6–1.0 nm, showed the highest CO yield (38% at 500 °C) with balanced CO 2 conversion and CO selectivity. Transient CO 2 hydrogenation and temperature-programmed surface reaction (TPSR) studies suggested that the adsorbed CO 2 species participated in CO 2 hydrogenation. On Ru 1 sites, CO 2 hydrogenation followed the RWGS pathway, resulting in the production of CO. In contrast, on Ru FAC sites, the enhanced H 2 dissociation ability, along with the presence of adsorbed bidentate and monodentate carbonate species at the Ru-MgO interfaces, facilitated the formation of CH 4 through the CO 2 methanation pathway. In conclusion, this study highlights the critical roles of Ru structure and local environment in defining the CO 2 hydrogenation pathways and provides new design principles for highly active Ru-based catalysts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

In planta production of the nylon precursor beta-ketoadipate

Beta-ketoadipate (βKA) is an intermediate of the βKA pathway involved in the degradation of aromatic compounds in several bacteria and fungi. Beta-ketoadipate also represents a promising chemical for the manufacturing of performance-advantaged nylons. We established a strategy for the in planta synthesis of βKA via manipulation of the shikimate pathway and the expression of bacterial enzymes from the βKA pathway. Using Nicotiana benthamiana as a transient expression system, we demonstrated the efficient conversion of protocatechuate (PCA) to βKA when plastid-targeted bacterial-derived PCA 3,4-dioxygenase (PcaHG) and 3-carboxy-cis,cis-muconate cycloisomerase (PcaB) were co-expressed with 3-deoxy-D-arabinoheptulosonate 7-phosphate synthase (AroG) and 3-dehydroshikimate dehydratase (QsuB). This metabolic pathway was reconstituted in Arabidopsis by introducing a construct (pAtβKA) with stacked pcaG, pcaH, and pcaB genes into a PCA-overproducing genetic background that expresses AroG and QsuB (referred as QsuB-2). The resulting QsuB-2 x pAtβKA stable lines displayed βKA titers as high as 0.25 % on a dry weight basis in stems, along with a drastic reduction in lignin content and improvement of biomass saccharification efficiency compared to wild-type controls, and without any significant reduction in biomass yields. Using biomass sorghum as a potential crop for large-scale βKA production, techno-economic analysis indicated that βKA accumulated at titers of 0.25 % and 4 % on a dry weight basis could be competitively priced in the range of $2.04-34.49/kg and $0.47-2.12/kg, respectively, depending on the selling price of the residual biomass recovered after βKA extraction. This study lays the foundation for a more environmentally-friendly synthesis of βKA using plants as production hosts.

Kazaz, Sami↗
DOE OSTI2025

PFOA catalytic reaction mechanisms on zerovalent iron (Fe 0 ): A DFT investigation

In this study, density functional theory (DFT) calculations with dispersion corrections are employed to investigate catalytic reactions of perfluorooctanoic acid (PFOA) onto zerovalent iron (Fe 0 ). The main goal of this investigation is to explain the reaction mechanisms, including bond dissociation energies, activation barriers, and rate-determining steps (RDSs), of PFOA degradation. Additionally, we aim to reveal the catalytic effects of Fe 0 by comparing the reaction energy profile for the degradation of PFOA both in solution (i.e., isolated) and after adsorption on Fe 0 . Along with investigating previously reported pathways, this study proposes a new PFOA degradation pathway on Fe0. Overall, the results revealed that Fe 0 plays a key role in the catalytic degradation of PFOA, significantly affecting the RDSs and increasing defluorination rates. For instance, the activation barrier for the decarboxylation step significantly decreased from 3.08 eV to 1.11 eV over the Fe0 surface, while the activation barrier for F dissociation decreased from ∼5 eV to 0.54 eV. Additionally, the proposed pathway in this study (i.e., successive defluorination) was found to be the most favorable pathway for PFOA degradation on Fe 0 . Taken together, the DFT results are consistent with reported experimental findings and provide critical insights that will help advance the design of catalysts for PFAS degradation.

Catalysis↗
DOE OSTI2026

An Analysis of Energy Needs and Seawater Extraction Approaches for the Integration of Primary Magnesium Production with Nuclear Power

The cost of primary magnesium production is highly dominated by the energy required to produce the metal. This, along with the current geographical concentration of its production, makes the magnesium price vulnerable as energy-production paradigms begin to rapidly change. In this work, four nuclear-integration pathways for the efficient supply of heat and electricity to magnesium production from a nuclear power plant are considered. A production route using electrified metallothermic reduction is compared to a nuclear-heat-integrated electrolytic pathway. It is shown that the latter can achieve significantly lower primary energy consumption, 261 MJ/kg Mg compared with 416 MJ/kg Mg. The electrolytic pathway can also reduce emissions down to around 2.1 kgCO2/kg Mg, compared to around 34 kgCO2/kg Mg in the Pidgeon process. Beyond energy and emissions, the four pathways considered are also compared to their ability to reduce locational dependence of the production plant and reduce process complexity. This work also highlights future advances in magnesium production with a potential scheme for the efficient extraction of magnesium from seawater with coproduction of desalinated water and the potential of demand-side response from magnesium electrolysis. This is the first work to consider the full integration of primary magnesium production using nuclear cogeneration, and it is hoped the study paves the way for the analysis of economic nuclear integration within metal extraction and manufacturing.

22 - GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2025

Indicators of carbon alteration (ICAs) suggest patterns in reservoir methane emissions

Reservoir operations influence emissions via multiple causal pathways. In this paper, we quantify indicators of carbon alteration (ICAs) focused on methane. ICAs were chosen to reflect the potential for methane emission along four causal pathways: 1) water column mixing, 2) wet-dry cycles in sediment, 3) sediment redistribution, and 4) vegetation. We developed algorithms to calculate ICAs for three reservoirs along a longitudinal gradient in the Tennessee River basin of the southeast US. The ICAs revealed interesting longitudinal patterns. Indicators of both methane production and destruction increased downstream. The potential for ebullitive methane emissions driven by sub-daily water level fluctuations and emissions mediated by vegetation were higher in downstream mainstem reservoirs than in the upstream tributary reservoir. Along the remaining two pathways, longitudinal patterns were equivocal (sediment pathway) or suggested decreased emissions downstream (water-column mixing). We also observed seasonal patterns and, by combining ICAs, inferred times when ramping could be achieved with lower risk of emissions. The ICAs demonstrated here are the first step in quantifying mechanistic relationships between reservoir operation and methane emissions. In future, they may lead to improved operations in reservoir cascades and regional-scale estimates of emissions that account for differences among reservoirs.

Greenhouse gases↗
DOE OSTI2025

Effects of co-adsorbed water on different bond cleavages involved in acetic acid decomposition on Pt (111)

Acetic acid decomposition on Pt (111) in the presence of co-adsorbed water is a good model system for oxygenate decomposition on Pt (111) in aqueous phase, with application in hydrogen production and biomass conversion. Here, in this study, we present a density functional theory (DFT) theory calculation of how co-adsorbed water affects different bond cleavages of acetic acid decomposition on Pt (111). The presence of co-adsorbed water generally enhances O$-$H bond cleavage while inhibiting OC$-$O and OC$-$OH bond cleavage. The influence of co-adsorbed water on C$-$H bond cleavage varies the most and depends on the nature of the transition state and how co-adsorbed water stabilizes the initial and final state. Although these trends are useful as general guidance, they are not sufficient to predict the effect on a complex reaction network such as acetic acid decomposition on Pt (111) which has several parallel reaction paths with similar energies. In the absence of co-adsorbed water, the two lowest energy pathways are decarboxylation (DCX) and decarbonylation (DCN) pathways through a common CH 2 COO intermediate, in which the DCX pathway (C$-$H bond cleavage of CH 2 COO) is more favorable than DCN pathway (OC$-$O bond cleavage of CH 2 COO). In the presence of co-adsorbed water, the energy difference between Csingle bondH bond cleavage and OC$-$O bond cleavage of CH 2 COO increases, suggesting an increase in the favorability of acetic acid decarboxylation (formation of carbon dioxide) over acetic acid decarbonylation (formation of carbon monoxide) on Pt (111).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

BEAST DB: Grand-Canonical Database of Electrocatalyst Properties

We present BEAST DB, an open-source database comprised of ab initio electrochemical data computed using grand-canonical density functional theory in implicit solvent at consistent calculation parameters. The database contains over 20,000 surface calculations and covers a broad set of heterogeneous catalyst materials and electrochemical reactions. Calculations were performed at self-consistent fixed potential as well as constant charge to facilitate comparisons to the computational hydrogen electrode. This article presents common use cases of the database to rationalize trends in catalyst activity, screen catalyst material spaces, understand elementary mechanistic steps, analyze the electronic structure, and train machine learning models to predict higher fidelity properties. Users can interact graphically with the database by querying for individual calculations to gain a granular understanding of reaction steps or by querying for an entire reaction pathway on a given material using an interactive reaction pathway tool. BEAST DB will be periodically updated, with planned future updates to include advanced electronic structure data, surface speciation studies, and greater reaction coverage.

database↗
DOE OSTI2025

Automatic Generation of Chemical Mechanisms for Electrochemical Systems: Solid Electrolyte Interphase Formation in Lithium Batteries

Electrolytes in many lithium ion batteries decompose at the low potentials near the anode. The decomposition products form a layer termed the solid electrolyte interphase (SEI). The composition and growth of the SEI layer significantly affect both the capacity fade and safety of lithium ion batteries. However, SEI formation and growth kinetics are not well understood. In this work, we present an extension of the Reaction Mechanism Generator (RMG) software to automatically generate mechanisms for SEI formation. We extend RMG’s solvation correction framework to account for kinetic solvent effects and demonstrate the accuracy of our technique. We calculate thermochemical parameters for 252 species and rate coefficients for 69 reactions, most with associated solvation corrections. This and additional quantum chemistry data are used to extend RMG’s thermodynamic group additivity and solute parameter estimation schemes to handle lithiated species and add 14 new reaction families to RMG. RMG is additionally extended to simulate electrocatalytic systems. Lastly, we demonstrate RMG on the decomposition of acetonitrile and ethylene carbonate near a battery anode. Furthermore, while this framework does not yet resolve individual ions, as appropriate thermochemistry estimators are not available, and thus, cannot yet resolve more complex electrochemical pathways, RMG is able to generate reasonable pathways for SEI formation that match literature pathways and products. In particular, RMG identifies a new important reaction pathway that is not present in literature.

Chemical reactions↗
DOE OSTI2026

Multiscale Characterization of Electrode-Induced Degradation in Perovskite Solar Cells

The stability of metal-halide-perovskite (MHP) solar cells must be understood and improved for the commercial viability of MHP technologies. Here, we apply multiscale characterization methods to study degradation modes, specifically electrode corrosion, for p-i-n MHP partial device stacks and full devices that are stored in the dark under an inert atmosphere. Our multiscale characterization approaches include full-device electro-optical performance using current-voltage (JV) curves and spatial imaging with electroluminescence (EL) and photoluminescence (PL). We further correlate interface properties using cross-sectional Kelvin probe force microscopy, which maps the nanoscale electric field properties, and electron microscopy, which demonstrates structural and chemical features. Devices stored as a full device stack degrade primarily by metal (Ag) electrode diffusion into the absorber, with formation of AgI byproducts and Ag accumulation near the indium tin oxide (ITO) contact. This causes decomposition of the perovskite absorber domains, loss of the potential drop at the electron transport layer (ETL)/perovskite interface near the metal contact, and increased equivalent resistance at the perovskite/hole transport layer (HTL) interface near the ITO contact. The devices stored without metal show a different degradation pathway dominated by corrosion of the ITO, creating voids at the ITO electrode surface with diffusion of In and Sn into the absorber. We conclude that metal electrode-induced degradation is the most severe degradation pathway under dark storage, but that ITO corrosion and absorber instability must also be mitigated. We further demonstrate mitigation of these degradation pathways by changes to the device stack, including a SnO x blocking layer at the ETL side and replacing ITO with FTO at the HTL side. These results provide a useful demonstration of specific dark degradation pathways at each electrode interface, as well as a unique multiscale example that links degradation of chemical, structural, and electrical interface properties to the full-device electro-optical characteristics.

14 SOLAR ENERGY↗
DOE OSTI2025

Machine Learning-Accelerated First-Principles Molecular Dynamics Reveals C–C Coupling Mechanisms toward Ethylene on Cu(100)

Here, the Cu(100) termination has been identified as the most effective facet for converting CO and CO 2 into ethylene. To enhance both the activity and selectivity of ethylene production, we perform machine-learning-accelerated, first-principles molecular dynamics simulations at 298 K in an explicit solvent at pH 7 to elucidate the C–C coupling mechanism─the critical reaction step in forming C 2+ products. Among the six potential C–C coupling pathways, the most feasible are CO* dimerization and CO – CHO* and CHO* – CHO* couplings. Using the computational hydrogen electrode method, we demonstrate that all three pathways are equally accessible at −0.6 V vs RHE. At a potential below −1.0 V vs RHE, the thermodynamic barriers for the CO – CHO* and CHO* – CHO* pathways become negligible. Our computational findings explain the experimental observations, particularly the absence of C 2+ products above −0.4 V vs RHE and the peaks in ethylene production near −0.6 and −1.0 V vs RHE. Since CHO* acts as a key intermediate common to both C–C coupling and CH 4 formation, we propose that suppressing CHO* hydrogenation would inhibit CH 4 pathways, thereby maximizing ethylene selectivity.

CO2 reduction↗
DOE OSTI2026

Effect of Strength of Soluble and Solid Acid Catalysts on Selectivity in Aldol Reactions

Aldol reactions can follow the classical condensation path and produce an α,β-unsaturated carbonyl compound and water, however in some cases, aldol chemistry may be steered towards a fission that gives an olefin and a carboxylic acid. This investigation examines how the strength of Brønsted acid sites—both in homogeneous and heterogeneous catalysis—controls these two pathways and their kinetics. The cross-aldol reaction between benzaldehyde and 3-pentanone served as test case. Batch reactions, conducted in toluene as solvent at a temperature of 140 °C under autogenous pressure, were analyzed by GC and in situ ATR-FTIR spectroscopy to determine product distributions and rate constants for condensation and fission pathways. A series of soluble acids including a family of sulfonic acids mostly favored the condensation pathway, with formic acid as the weakest in the series by its pKa being inactive for aldol chemistry. Significant amounts of fission products were rare except for the known selectivity of phosphoric acid, and the circumstances were difficult to delineate. For the sulfonic acid family, the logarithm of the first-order condensation rate constants scaled only roughly with pKa (water) values, whereas a good correlation was obtained with calculated deprotonation Gibbs energies in toluene. A series of H-forms of isomorphously substituted beta zeolites, HESiBEA with E = Al, Ga, Fe, or B, favored the fission pathway. Site density and site strength were characterized by calorimetric measurements of the heats of adsorption of isopropylamine, which decreased in the order Al > Ga, Fe > B. The logarithm of the site-normalized first-order fission rate constants scaled roughly with the heats of adsorption and correlated excellently with reported deprotonation energies. In conclusion, acid strength mainly affects activity and can be seen as a pre-requisite for either aldol condensation or fission chemistry, whereas additional, yet to be full clarified catalyst properties and reaction conditions are required to steer aldol chemistry towards fission selectivity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Anthropogenic extremely low volatility organics (ELVOCs) Govern the Growth of Molecular Clusters over the Southern Great Plains during the Springtime

New particle formation (NPF) and growth govern cloud condensation nuclei (CCN) concentrations in many regions. The mechanisms governing the nucleation of molecular clusters vary substantially in different regions of the atmosphere. Additionally, the growth of these clusters from ~2 to 20 nm sizes is often governed by the availability of extremely low volatility organic vapours (ELVOCs). While the pathways to ELVOC formation from the oxidation of biogenic monoterpenes with ozone is better understood, the chemical and mechanistic pathways for ELVOC formation from oxidation of anthropogenic organics are not well understood. We integrate measurements and three-dimensional regional model simulations with the Weather Research and Forecasting Model coupled to chemistry (WRF-Chem) to understand the processes governing new particle formation and growth and secondary organic aerosol (SOA) formation during the Holistic Interactions of Shallow Clouds, Aerosols and Land Ecosystems (HI-SCALE) field campaign at the Southern Great Plains (SGP) observatory in Oklahoma, and contrast it with a site within the Bankhead National Forest (BNF), Alabama in Southeast USA, where 5-year long measurements will begin in 2024. Simulations show that nucleation rates are at least an order of magnitude higher at SGP compared to BNF during the springtime days (April 28 and May 14, 2016), largely due to lower H2SO4 concentrations at BNF, which are needed for nucleation. In addition, the larger CS at BNF (compared to SGP) increase the loss of molecular clusters by coagulation to pre-existing particles. Among the 8 different nucleation mechanisms in WRF-Chem, we find that the amine+H2SO4 nucleation mechanism dominates at the SGP site, while the pure organic ion induced nucleation mechanism dominates over BNF. Through various WRF-Chem sensitivity simulations, we find that anthropogenic ELVOCs are critical for explaining the growth of newly formed particles and the resulting number size distribution observed near the surface at the SGP site during the daytime. In addition, we show that treating organic particles as semisolid, with strong diffusion-limited uptake of organic vapours, brings model predictions into closer agreement with the observed evolution of particle size distribution. Simulations also predict that anthropogenic SOA, formed by the oxidation of aromatic volatile organic compounds (VOCs), is the dominant organic aerosol component at SGP, while biogenic SOA dominates particle composition at the BNF site in Southeast USA on these days.

Shrivastava, ManishKumar B.↗
DOE OSTI2025

Discovery of FoTO1 and Taxol genes enables biosynthesis of baccatin III

Abstract Plants make complex and potent therapeutic molecules 1,2 , but sourcing these molecules from natural producers or through chemical synthesis is difficult, which limits their use in the clinic. A prominent example is the anti-cancer therapeutic paclitaxel (sold under the brand name Taxol), which is derived from yew trees (Taxusspecies) 3 . Identifying the full paclitaxel biosynthetic pathway would enable heterologous production of the drug, but this has yet to be achieved despite half a century of research 4 . WithinTaxus’ large, enzyme-rich genome 5 , we suspected that the paclitaxel pathway would be difficult to resolve using conventional RNA-sequencing and co-expression analyses. Here, to improve the resolution of transcriptional analysis for pathway identification, we developed a strategy we term multiplexed perturbation × single nuclei (mpXsn) to transcriptionally profile cell states spanning tissues, cell types, developmental stages and elicitation conditions. Our data show that paclitaxel biosynthetic genes segregate into distinct expression modules that suggest consecutive subpathways. These modules resolved seven new genes, allowing a de novo 17-gene biosynthesis and isolation of baccatin III, the industrial precursor to Taxol, inNicotiana benthamianaleaves, at levels comparable with the natural abundance inTaxusneedles. Notably, we found that a nuclear transport factor 2 (NTF2)-like protein, FoTO1, is crucial for promoting the formation of the desired product during the first oxidation, resolving a long-standing bottleneck in paclitaxel pathway reconstitution. Together with a new β-phenylalanine-CoA ligase, the eight genes discovered here enable the de novo biosynthesis of 3’-N-debenzoyl-2’-deoxypaclitaxel. More broadly, we establish a generalizable approach to efficiently scale the power of co-expression analysis to match the complexity of large, uncharacterized genomes, facilitating the discovery of high-value gene sets.

Science & Technology - Other Topics↗
DOE OSTI2024

Investigating the mechanism of chloroplast singlet oxygen signaling in the Arabidopsis thaliana accelerated cell death 2 mutant

As sessile organisms, plants have evolved complex signaling mechanisms to sense stress and acclimate. This includes the use of reactive oxygen species (ROS) generated during dysfunctional photosynthesis to initiate signaling. One such ROS, singlet oxygen ( 1 O 2 ), can trigger retrograde signaling, chloroplast degradation, and programmed cell death. However, the signaling mechanisms are largely unknown. Several proteins (e.g. PUB4, OXI1, EX1) are proposed to play signaling roles across three Arabidopsis thaliana mutants that conditionally accumulate chloroplast 1 O 2 (fluorescent in blue light (flu), chlorina 1 (ch1), and plastid ferrochelatase 2 (fc2)). We previously demonstrated that these mutants reveal at least two chloroplast 1 O 2 signaling pathways (represented by flu and fc2/ch1). Here, we test if the 1 O 2 -accumulating lesion mimic mutant, accelerated cell death 2 (acd2), also utilizes these pathways. The pub4–6 allele delayed lesion formation in acd2 and restored photosynthetic efficiency and biomass. Conversely, an oxi1 mutation had no measurable effect on these phenotypes. acd2 mutants were not sensitive to excess light (EL) stress, yet pub4–6 and oxi1 both conferred EL tolerance within the acd2 background, suggesting that EL-induced 1 O 2 signaling pathways are independent from spontaneous lesion formation. Thus, 1 O 2 signaling in acd2 may represent a third (partially overlapping) pathway to control cellular degradation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Arabidopsis cytochrome b 5 proteins support fatty acid ω-3 but not ω-6 desaturation

Fatty acids are primary components of lipids, which serve as major energy sources in cells and play essential roles in membrane structure, signaling, and metabolic regulation (Shanklin and Cahoon 1998). The degree of fatty acid unsaturation critically influences lipid physicochemical properties, thereby affecting membrane fluidity and biological function (Nguyen et al. 2019). In Arabidopsis thaliana, fatty acid desaturation occurs via 2 parallel pathways: the “prokaryotic pathway” in plastids, involving glycosylglycerides, such as monogalactosyldiacylglycerol (MGDG) and digalactosyldiacylglycerol (DGDG), and phospholipid phosphatidylglycerol (PG); and the “eukaryotic pathway” in the endoplasmic reticulum (ER), involving phosphatidylcholine (PC) (Lou et al. 2014) (Supplementary Figure S1). Seven fatty acid desaturases (FADs) in Arabidopsis differentially desaturate each glycerolipid class in the plastid and ER (Nguyen et al. 2019). FAD2, an ER-resident ω-6 fatty acid desaturase, catalyzes the conversion of oleic acid (18:1) to linoleic acid (18:2), which can be further desaturated to α-linolenic acid (18:3) by FAD3, an ER-resident ω-3 fatty acid desaturase. In plastids, FAD6 catalyzes the desaturation of 18:1/16:1 to produce 18:2/16:2, while FAD7 and FAD8 redundantly convert 18:2/16:2 to 18:3/16:3 (Li-Beisson et al. 2013; Nguyen et al. 2019). Additionally, fatty acids synthesized in the ER can also be reimported into plastids to their site of de novo synthesis (Xu et al. 2010). All FADs require reducing power, in the form of 2 electrons, for catalysis, but the sources of the electrons vary between their subcellular localizations. In the ER, FAD2 and FAD3 receive electrons from a cytochrome b 5 (CB5)-based electron transfer chain comprising cytochrome b 5 reductase (CBR) and CB5. In contrast, ferredoxin serves as the electron donor for plastid-localized FAD6, FAD7, and FAD8 (Ohlrogge and Browse 1995; Andreu et al. 2007). While the relative contributions of the 2 pathways to total cellular desaturation products vary across tissues and species, most polyunsaturated FA biosynthesis in seeds occurs via ER-resident FAD2 and FAD3 (Miquel and Browse 1992; Ohlrogge and Browse 1995).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Multi-Omics Reveals Temporal Scales of Carbon Metabolism in Synechococcus Elongatus PCC 7942 Under Light Disturbance

Central carbon metabolism in model cyanobacteria involves multiple pathways to adapt to energy-light limitations across diel cycles. However, the success in mechanistic modeling for phenotypic prediction of the protein regulators in the metabolic state depends on capturing the vast possibilities emerging from multiple regulatory pathways in complex biological processes. Here, we developed a physics-informed machine learning approach based on energy-landscape concepts to predict regulatory proteins responding to cyclic circadian and unforeseen light perturbations in cyanobacterial metabolic networks. Our approach provides interpretable de novo models for inferring gene expression dynamics from Synechococcus elongatus over diel cycles and using redox proteome analysis to distinguish immediate light-responsive elements from circadian-regulated processes in carbon metabolism pathways. We identified distinct temporal signatures with the analysis of the redox proteome: there was an immediate shift in cysteine redox states accompanied by a limited change in protein abundance under constant illumination and after 2 hours of darkness. This discovery indicates that the generation of reductants coordinates photoinduced electron transport with redox metabolic pathways in two discernable molecular mechanisms: fast redox-based protein modifications occur immediately after the light disturbance, followed by slow transcriptional regulations across networks. This temporal regulation reveals how metabolic networks integrate rapid light responses with programmed circadian rhythms to maintain cellular homeostasis under the light-energy limitations over the diel cycle.

Biomolecular & subcellular processes↗
DOE OSTI2024

Diverse fates of ancient horizontal gene transfers in extremophilic red algae

Abstract Horizontal genetic transfer (HGT) is a common phenomenon in eukaryotic genomes. However, the mechanisms by which HGT‐derived genes persist and integrate into other pathways remain unclear. This topic is of significant interest because, over time, the stressors that initially favoured the fixation of HGT may diminish or disappear. Despite this, the foreign genes may continue to exist if they become part of a broader stress response or other pathways. The conventional model suggests that the acquisition of HGT equates to adaptation. However, this model may evolve into more complex interactions between gene products, a concept we refer to as the ‘Integrated HGT Model’ (IHM). To explore this concept further, we studied specialized HGT‐derived genes that encode heavy metal detoxification functions. The recruitment of these genes into other pathways could provide clear examples of IHM. In our study, we exposed two anciently diverged species of polyextremophilic red algae from the Galdieria genus to arsenic and mercury stress in laboratory cultures. We then analysed the transcriptome data using differential and coexpression analysis. Our findings revealed that mercury detoxification follows a ‘one gene‐one function’ model, resulting in an indivisible response. In contrast, the ars H gene in the arsenite response pathway demonstrated a complex pattern of duplication, divergence and potential neofunctionalization, consistent with the IHM. Our research sheds light on the fate and integration of ancient HGTs, providing a novel perspective on the ecology of extremophiles.

59 BASIC BIOLOGICAL SCIENCES↗