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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Data for High Yield Production of 3-Hydroxypropionic Acid Using Issatchenkia orientalis

Biomanufacturing provides a more sustainable alternative to fossil-based chemical manufacturing. 3-Hydroxypropionic acid (3HP) is a top Department of Energy value-added chemical and precursor to bioplastics, yet cost-effective microbial production remains elusive. Here, we establish the acid-tolerant yeast Issatchenkia orientalis as a robust host for low-pH 3HP biosynthesis. Genome-scale modeling identifies the β-alanine pathway as optimal, offering the highest theoretical yield and lowest oxygen requirement. Thermodynamic analysis confirms its favorability under acidic conditions. Using sequence similarity network analysis, we discover highly active aspartate 1-decarboxylase (PAND), β-alanine-pyruvate aminotransferase (BAPAT), and 3HP dehydrogenase (YDFG), which significantly improve the pathway efficiency. Next, to further elevate the production, pathway optimization through multi-copy PAND integration, byproduct elimination (knockouts of pyruvate decarboxylase and glycerol-3-phosphate dehydrogenase), and reinforcement of aspartate flux by overexpression of pyruvate carboxylase and aspartate amino transferase improves the titer to 29 g/L in shake flasks. Fed-batch fermentation at pH 4 with low-cost corn steep liquor medium further increases the production to 92 g/L with 0.7 g/g yield and 0.55 g/L/h productivity. Techno-economic analysis indicates that such performance could potentially enable a financially viable process for sustainable acrylic acid production. This work establishes I. orientalis as a next-generation platform for cost-effective 3HP production and paves the way toward industrial commercialization.

Bioproducts↗
DOE OSTI2024

Influence of alloy solidification path on melt pool behavior in additive manufacturing

Numerical models used to study transport phenomena in laser-powder bed fusion processes often rely on assumptions and simplifications to reduce their computational expense. One common simplification is in the description of latent heat evolution during the solid-liquid phase change (i.e., the solidification pathway), justified by the fact that the mushy zone thickness is similar to the numerical grid spacing used for continuum transport models. The lack of resolution of transport phenomena in the mushy zone motivates the use of computationally convenient solidification paths such as linear or sigmoidal relationships over pathways derived from fundamental solidification theory such as equilibrium or Scheil models. In the present work, an uncertainty quantification (UQ) framework is used to analyze the influence of solidification pathway selection on the solidification dynamics and melt pool geometries in laser based additive manufacturing (AM) of IN625. Results show the solidification pathway has a quantifiable influence on the cooling rate at the liquidus isotherm, mushy zone thickness, and solidification time. Due to similarities in the latent heat evolution at the beginning of solidification, the equilibrium and Scheil models predict similar cooling rates near the liquidus isotherm, however the wider freezing range of Scheil leads to a wider mushy zone compared to equilibrium. The non-physical latent heat release profiles of sigmoidal and linear paths lead to significant overpredictions of cooling rates at the liquidus isotherm compared to equilibrium and Scheil. Finally, these results indicate that careful consideration should be given to the choice of solidification pathway to ensure reliable model predictions.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Lyotropic Liquid Crystal Mediated Assembly of Donor Polymers Enhances Efficiency and Stability of Blade-Coated Organic Solar Cells

Conjugated polymers can undergo complex, concentration-dependent self-assembly during solution processing, yet little is known about its impact on film morphology and device performance of organic solar cells. Herein, lyotropic liquid crystal (LLC) mediated assembly across multiple conjugated polymers is reported, which generally gives rise to improved device performance of blade-coated non-fullerene bulk heterojunction solar cells. Using D18 as a model system, the formation mechanism of LLC is unveiled employing solution X-ray scattering and microscopic imaging tools: D18 first aggregates into semicrystalline nanofibers, then assemble into achiral nematic LLC which goes through symmetry breaking to yield a chiral twist-bent LLC. The assembly pathway is driven by increasing solution concentration – a common driving force during evaporative assembly relevant to scalable manufacturing. This assembly pathway can be largely modulated by coating regimes to give 1) lyotropic liquid crystalline assembly in the evaporation regime and 2) random fiber aggregation pathway in the Landau–Levich regime. The chiral liquid crystalline assembly pathway resulted in films with crystallinity 2.63 times that of films from the random fiber aggregation pathway, significantly enhancing the T80 lifetime by 50-fold. The generality of LLC-mediated assembly and enhanced device performance is further validated using polythiophene and quinoxaline-based donor polymers.

14 SOLAR ENERGY↗
DOE OSTI2026

Linking DSC/TGA to Cell Levels: Energetics, Evolved Gases, and Thermal Safety of NMC811‐Graphite Micro‐Cell

Thermochemical characterization of battery materials links intrinsic material properties to decomposition pathways, heat generation, and gas evolution that govern performance and safety. Despite extensive work on NMC811-Graphite, variability across partial configurations and the limited adoption of micro-cell architectures (cathode+anode+electrolyte+separator) hinder robust cell-scale interpretation. Accordingly, this work establishes a bottom-up, component-resolved methodology integrating DSC/TGA, evolved gas analysis (EGA), and in situ XRD to link decomposition pathways and energy release across partial and micro-cell configurations, providing a transferable assessment of safety and stability in emerging chemistries. In separator-free configurations, the gas–solid reaction between cathode-evolved O 2 and anode-leached Li dominates the net heat release (1139 J g −1 ). In contrast, in the micro-cell configuration, the separator hinders O 2 transport and alters the timing and pathways of other reactions, and reduces the net energy release to 618 J g −1 . Energy release was organized into defined temperature windows that provide a framework for a thermodynamic model combining quantified gas evolution with selected decomposition pathways and effective reaction enthalpies to estimate net specific energy release, with agreement between DSC and cell-level tests. Ex situ XPS of heat-treated samples extends post-mortem analysis to thermal-abuse regimes, supporting key pathway elements.

25 ENERGY STORAGE↗
DOE OSTI2026

Spin‐Polarized Interfaces Redirect CO 2 Reduction From CO to Formate

Achieving high product selectivity in electrocatalytic carbon dioxide reduction (CO 2 RR) remains a critical challenge due to competition between multiple proton-coupled electron-transfer pathways on catalyst surfaces. Meanwhile, chirality-induced spin selectivity (CISS), which enables spin-polarized electron transport through chiral interfaces, has recently emerged as a promising strategy to modulate interfacial electrochemical reactions. Although the CISS effect has been shown to enhance selectivity and efficiency in the spin-sensitive oxygen evolution reaction (OER), its role in regulating CO 2 RR pathways and in stabilizing intermediates remains largely unexplored. Here, chiral molecules (R- and S-1,1′-bi-2-naphthyl-2,2′-diyl hydrogen phosphate, BNP) were integrated with SnO 2 to construct chiral-modified catalysts (R-BNP/SnO 2 and S-BNP/SnO 2 ). Compared with bare SnO 2 and racemic BNP-modified SnO 2 (Rac-BNP/SnO 2 ), the chiral catalysts exhibited a pronounced shift in product selectivity from CO toward formate production. Importantly, in-situ attenuated total reflectance surface-enhanced infrared absorption spectroscopy (ATR-SEIRAS) reveals that the chiral interface selectively stabilizes the O-bound *OCHO intermediate associated with the formate pathway and modulates interfacial water structure and hydrogen-bonding dynamics. These findings demonstrate that spin-polarized interfacial electron transfer can regulate CO 2 RR pathway selectivity by modulating the stabilization of key intermediates. More broadly, this work establishes chiral spin-selective interfaces as a new strategy for regulating competitive electrocatalytic reaction pathways.

14 SOLAR ENERGY↗
DOE OSTI2025

Hyperspectral leaf reflectance of grasses varies with evolutionary lineage more than with site

Abstract To predict ecological responses at broad environmental scales, grass species are commonly grouped into two broad functional types based on photosynthetic pathway. However, closely related species may have distinctive anatomical and physiological attributes that influence ecological responses, beyond those related to photosynthetic pathway alone. Hyperspectral leaf reflectance can provide an integrated measure of covarying leaf traits that may result from phylogenetic trait conservatism and/or environmental conditions. Understanding whether spectra‐trait relationships are lineage specific or reflect environmental variation across sites is necessary for using hyperspectral reflectance to predict plant responses to environmental changes across spatial scales. We measured hyperspectral leaf reflectance (400–2400 nm) and 12 structural, biochemical, and physiological leaf traits from five grass‐dominated sites spanning the Great Plains of North America. We assessed if variation in leaf reflectance spectra among grass species is explained more by evolutionary lineage (as captured by tribes or subfamilies), photosynthetic pathway (C 3 or C 4 ), or site differences. We then determined whether leaf spectra can be used to predict leaf traits within and across lineages. Our results using redundancy analysis ordination (RDA) show that grass tribe identity explained more variation in leaf spectra (adjusted R 2 = 0.12) than photosynthetic pathway, which explained little variation in leaf spectra (adjusted R 2 = 0.00). Furthermore, leaf reflectance from the same tribe across multiple sites was more similar than leaf reflectance from the same site across tribes (adjusted R 2 = 0.12 and 0.08, respectively). Across all sites and species, trait predictions based on spectra ranged considerably in predictive accuracies ( R 2 = 0.65 to <0.01), but R 2 was >0.80 for certain lineages and sites. The relationship between Vc max , a measure of photosynthetic capacity, and spectra was particularly promising. Chloridoideae, a lineage more common at drier sites, appears to have distinct spectra‐trait relationships compared with other lineages. Overall, our results show that evolutionary relatedness explains more variation in grass leaf spectra than photosynthetic pathway or site, but consideration of lineage‐ and site‐specific trait relationships is needed to interpret spectral variation across large environmental gradients.

Pau, Stephanie [Department of Geography University↗
DOE OSTI2024

The role of the iron and steel sector in achieving net zero U.S. CO 2 emissions by 2050

The U.S. steel sector is a hard-to-abate sector because of its heavy dependence on fossil fuels and its high capital requirements. In 2015, the sector was one of the major carbon emitters, contributing 10 % of the U.S. industrial CO 2 emissions. The ability to decarbonize the U.S. iron and steel sector directly affects the ability of the U.S. to achieve economy-wide net zero CO 2 by 2050. In this paper, we use the Global Change Analysis Model (GCAM) to analyze different U.S. steel sector decarbonization pathways under varying technology, policy, and demand futures. These pathways provide insights on how various low-carbon steelmaking technologies such as those using carbon capture and storage (CCS), hydrogen, or scrap could help reduce U.S. steel emissions by mid-century. In our primary decarbonization pathway, we find that nearly all of the conventional fossil-based steelmaking capacity is fully integrated with CCS by 2050. However, without CCS availability, almost all of the conventional fossil-based steelmaking is phased-out by 2050 and is replaced by hydrogen-based production. Scrap-based production continues to remain vital across both of these decarbonization pathways. Furthermore, we find that demand reduction could help reduce the required levels of CCS and hydrogen-based production in the decarbonization pathways. Implementation of advanced energy efficiency measures could help substantially reduce the sector's energy usage. Finally, we observe that addressing the embodied carbon transfer associated with steel imports will be crucial for fully decarbonizing the U.S. steel sector.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Health and air pollutant emission impacts of net zero CO2 by 2050 scenarios from the energy modeling forum 37 study

Carbon dioxide and non-greenhouse gas air pollutants are emitted from many of the same sources. Decarbonization actions thus typically yield air pollutant emission reductions, resulting in significant air quality benefits. Although several studies have highlighted this connection, including in the context of net zero carbon emission targets, substantial uncertainty remains regarding how alternative technological pathways to this goal will affect the spatial distribution and magnitude of air pollutants. Comprehensive multi-model and multi-scenario analyzes are needed to explore the relative impacts of alternative pathways. Here, our study begins to address this gap by leveraging the results from the recent Energy Modeling Forum 37 inter-model comparison exercise on U.S. decarbonization pathways. Comparing the results of the six teams who submitted air pollutant emissions suggests that strategies that target net zero U.S. carbon emissions would yield significant reductions in many air pollutants, and that this finding is generally robust across pathways. However, some energy sources, such as biomass and fossil fuels with carbon capture, will emit air pollutants and can potentially influence the magnitude, spatial distribution, and even sign of localized air pollutant emission changes. In the second part of this analysis, a simplified air quality and health impacts screening model is used to evaluate the air quality impacts in 2035 of sectoral emission changes from the three models that provided sectoral detail. Relative to a reference scenario, a net zero pathway is estimated to reduce fine particulate matter concentrations across the contiguous U.S., with health benefits from reduced mortality ranging from $\$$65 billion to $\$$250 billion in 2035 alone (2023$\$$s). These benefits would be expected to grow over time as the net zero trajectory becomes more stringent. Both the magnitude of potential benefits and the substantial variation of the projections across models underscore the need for an EMF-like inter-model comparison exercise focused on air quality.

Air pollutants↗
DOE OSTI2026

Impact of DMP-30 catalyst concentration on the degradation and kinetics of bisphenol A epoxy thermosets cured with linear amine hardener

Epoxy thermosets are a crucial component in carbon-fiber composites, serving as the organic binding matrix. Catalysts are commonly used in prepolymer formulations to accelerate curing of the thermosets. However, the impact of catalysts on the thermal stability, degradation pathways, and kinetics of the final thermoset is poorly understood. Here, in this work, Product-Specific Kinetics (PSK) analysis was utilized with isoconversional kinetics to provide a first look into the degradation kinetics of major pyrolysis pathways in bisphenol A (BPA) epoxy resins and determine the impact of altering catalysis concentrations on these kinetic pathways. Results revealed new insights into previously identified degradation pathways, provided evidence of multiple degradation pathways for some products, and showed that use of excess catalyst results in polymer network alterations and reduced thermal stability of the thermosets.

Bisphenol A↗
DOE OSTI2025

Opportunity Assessment for Sustainable Aviation Fuel Production from Woody Biomass via Ex Situ Catalytic Fast Pyrolysis and Refinery Hydroprocessing

Biofuels have become a promising solution to reduce emissions in hard-to-electrify transportation sectors, such as aviation. However, several biofuel conversion pathways will likely be needed to scale sustainable aviation fuel (SAF) production to meet lower carbon intensity goals when biomass feedstock availability constraints are considered. This study evaluates the future potential of the catalytic fast pyrolysis (CFP) pathway to contribute to U.S. SAF production goals as outlined in the U.S. Department of Energy’s (DOE) SAF Grand Challenge, understanding that the CFP pathway is still under development toward maturity and scaleup. National forestland resource data from the DOE’s 2023 Billion Ton Study are integrated with recent experimental results demonstrating end-to-end woody biomass conversion to SAF via CFP and hydroprocessing in a novel bioeconomy optimization framework. U.S. refinery hydroprocessing capacity is also considered with repurposing and coprocessing strategies. Results indicate that the CFP process can contribute up to 4.6 billion gallons of SAF annually by 2040, meeting 13% of the 2050 SAF Grand Challenge target while reducing the carbon intensity (CI) of the U.S. jet fuel pool by 16%. The study further explores optimal processing strategies, suggesting that colocating CFP operations with existing petroleum refineries and repurposing some U.S. hydrocracking capacity may offer significant cost advantages and enhance the commercial viability of the CFP pathway. These results underscore the CFP pathway’s potential to support the global aviation industry’s lower carbon intensity objectives while producing other renewable fuels and products.

09 BIOMASS FUELS↗
DOE OSTI2025

Degrees of Rate Control in Interconnected Reaction Networks

Overall reactions in interconnected networks exhibit net, forward, and reverse rates that are governed by both constitutive elementary steps in the pathway of interest and branching elementary steps that lead to alternative products. Accordingly, steps in branching pathways exhibit negative net, forward, and reverse degrees of rate control, as they reduce reaction flux to the desired product. We here contextualize the forward and reverse degrees of rate control in terms of kinetic resistances (inverse of rates) and leverage the additive nature of kinetic resistance to decouple kinetic driving forces contributed by constitutive elementary steps and branching points (nodal species) in interconnected networks. Regardless of the network connectivity, forward and reverse degrees of rate control are shown to converge at equilibrium. Away from equilibrium, we identify two critical features of interconnected networks: stoichiometric regularity─condition where all stoichiometric numbers are unity─and pathway symmetry around nodal species─condition where branching pathways share the same rate constants, stoichiometry, and species concentrations/activities─that result in (i) equal forward, reverse, and consequently net degrees of rate control and (ii) forward and reverse degrees of rate control that exhibit constant offsets, respectively, across all extents of reaction. Furthermore, our discourse further provides a mathematical description for the influence of stoichiometric irregularity and pathway asymmetry on forward and reverse degrees of rate control. Altogether, the presented work details the effects of network (inter)connectivity and stoichiometry on reaction kinetics and, in doing so, establishes general protocols for capturing these effects as additive terms in the formulation of forward and reverse degrees of rate control.

10 SYNTHETIC FUELS↗
DOE OSTI2025

Cell-Free-Based Thermophilic Biocatalyst for the Synthesis of Amino Acids from One-Carbon Feedstocks

Bioproduction from one-carbon compounds, such as formate, is an attractive prospect due to reduced energy requirements and the possibility for using CO 2 as a sustainable feedstock. Formate-fixing pathways engineered using Escherichia coli lysate-based cell-free expression (CFE) biocatalysts have the potential to route 100% of feedstock carbon toward chemical synthesis but are undermined by siphoning of in-pathway metabolites and cofactors by the CFE background metabolism. To address this limitation, we engineer a CFE-based thermophilic multienzyme biocatalyst for the synthesis of serine and glycine from formate, bicarbonate, and ammonia. After expression of the thermophilic formate-to-serine pathway in a one-pot reaction, the mesophilic E. coli CFE background machinery is removed by simple heat denaturation, eliminating the siphoning of cofactors, inpathway metabolites, and products. After bioprocess optimization, including pathway gene expression duration and chemical synthesis temperature, we achieve near stoichiometric conversion of formate and bicarbonate to serine and glycine, reaching 97% of stoichiometric yield. The use of a moderately thermophilic biocatalyst allowed chemical synthesis to take place at mesophilic temperatures, enabling the balance of optimal enzyme activity with minimal metabolite/cofactor thermal degradation. In a fed-batch experiment, the biocatalyst shows sustained chemical synthesis rates for 8 h, paving the way toward a continuous bioprocess. Finally, a sensitivity analysis of cofactor usage revealed that the most expensive cofactors, THF and NADPH, can be reduced by 5-fold without significantly lowering product yields. To the best of our knowledge, this is the first instance of expressing a thermophilic pathway in an E. coli lysate-based CFE system to generate a thermophilic biocatalyst for use at mesophilic temperatures. The CFEbased thermophilic formate-to-serine biocatalyst triples the combined serine and glycine yield previously obtained by a CFE-based mesophilic formate-to-serine biocatalyst (30%), and quadruple the yield obtained by a purified enzyme system (22%). Ultimately, this work opens the door to using E. coli lysate-based CFE for thermophilic biocatalyst generation to achieve high chemical synthesis yields.

bacteria↗
DOE OSTI2025

From Nonclassical to Classical: Crystallization Seeds Reshape Nucleation Mechanisms

Crystalline seeds are widely employed in crystallization to accelerate nucleation and control product polymorphs; yet, their impact on nucleation mechanisms remains poorly understood. While homogeneous nucleation of crystals from solution often proceeds through nonclassical pathways involving amorphous intermediates, it is unclear how seeds that promote heterogeneous nucleation reshape these mechanisms and govern polymorph selection. Here, in this study, we provide the first direct evidence that crystalline seeds can bypass the need for amorphous intermediates as nucleation sites, converting nonclassical nucleation mechanisms into classical, monomer-by-monomer crystallization pathways. Using molecular dynamics simulations of zeolite synthesis, we uncover a complex reaction network of competing nucleation processes mediated by intermediate interfacial polymorphs. The interplay between thermodynamic stability and kinetic favorability of these interfacial polymorphs dictates nucleation outcomes, creating a dynamic balance between the interfacial polymorph stability and crystallization rates. Furthermore, we show that the synthesis environment-whether monomers or aggregates serve as reactants-profoundly impacts these pathways. At moderate supersaturation, seeds eliminate amorphous intermediates and promote classical nucleation, whereas high supersaturation or aggregate-based reactants favor nonclassical pathways, even in the presence of seeds. These findings establish a general framework for understanding how seeds govern crystallization mechanisms, with broad implications for controlling nucleation kinetics, polymorph selection, and material properties. While focused on zeolites, this work reveals insights that may be applicable to biominerals, pharmaceuticals, functional materials, and catalysts, providing a basis for engineering crystallization pathways in diverse applications.

Chu-Jon, Carlos [Univ. of Utah, Salt Lake City, UT↗
DOE OSTI2024

Rubisco activity and activation state dictate photorespiratory plasticity in Betula papyrifera acclimated to future climate conditions

Plant metabolism faces a challenge of investing enough enzymatic capacity to a pathway without overinvestment. As it takes energy and resources to build, operate, and maintain enzymes, there are benefits and drawbacks to accurately matching capacity to the pathway influx. The relationship between functional capacity and physiological load could be explained through symmorphosis, which would quantitatively match enzymatic capacity to pathway influx. Alternatively, plants could maintain excess enzymatic capacity to manage unpredictable pathway influx. In this study, we use photorespiration as a case study to investigate these two hypotheses in Betula papyrifera. This involves altering photorespiratory influx by manipulating the growth environment, via changes in CO 2 concentration and temperature, to determine how photorespiratory capacity acclimates to environmental treatments. Surprisingly, the results from these measurements indicate that there is no plasticity in photorespiratory capacity in B. papyrifera, and that a fixed capacity is maintained under each growth condition. The fixed capacity is likely due to the existence of reserve capacity in the pathway that manages unpredictable photorespiratory influx in dynamic environments. Additionally, we found that B. papyrifera had a constant net carbon assimilation under each growth condition due to an adjustment of functional rubisco activity driven by changes in activation state. These results provide insight into the acclimation ability and limitations of B. papyrifera to future climate scenarios currently predicted in the next century.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Glyceraldehyde-3-phosphate dehydrogenase homologs as bifunctional gatekeepers of metabolic segregation in Pseudomonas putida

Metabolically versatile Pseudomonas species can assimilate various glycolytic and gluconeogenic substrates. Simultaneous assimilation is known to segregate carbons from each substrate type into different metabolic pathways. However, the mechanisms of this metabolic segregation remain unresolved. Here, we investigate Pseudomonas putida KT2440 during processing of the sugar glucose through glycolysis versus the phenolic acid ferulate through gluconeogenesis. Metabolome profiling reveals up to twofold less tricarboxylic acid cycle metabolites but up to 10-fold higher metabolites of upper glycolysis, pentose-phosphate, and Entner–Doudoroff pathways in glucose-grown cells compared to ferulate-grown cells. After 13C-substrate switching, kinetic isotopic profiling captures rapid assimilation of new substrate carbons into initial catabolic pathways, but incorporation into downstream pathways is absent or incomplete. Proteomics identifies a 22-fold higher abundance of one homolog of glyceraldehyde-3-phosphate dehydrogenase (GAPDH, GapA) in cells fed on glucose relative to ferulate, while abundance of another homolog (GapB) remains unchanged. Growth phenotypes and quantitative metabolomics for single and double knockout mutants of these GAPDH homologs indicate only GapA involvement in glycolytic flux, which can be compensated by the Entner–Doudoroff pathway, and distinct preference of GapB with minimal role of GapA for gluconeogenic flux. Accordingly, growth of triple knockout mutant with deletion of gapA, gapB, and edd is possible only when glycolytic and gluconeogenic substrates are provided together to meet metabolic demands in a segregated fashion, but metabolic tradeoffs lead to slow growth. A mathematical, experimentally constrained, model of the GAPDH node shows that tuning of GapA and GapB concentrations enables transition between flux regimes for nutritional adaptability.

Zhou, Nanqing [Northwestern University, Evanston]↗
DOE OSTI2024

Biosensors for the detection of chorismate and cis,cis -muconic acid in Corynebacterium glutamicum

Abstract Corynebacterium glutamicum ATCC 13032 is a promising microbial chassis for industrial production of valuable compounds, including aromatic amino acids derived from the shikimate pathway. In this work, we developed two whole-cell, transcription factor based fluorescent biosensors to track cis,cis-muconic acid (ccMA) and chorismate in C. glutamicum. Chorismate is a key intermediate in the shikimate pathway from which value-added chemicals can be produced, and a shunt from the shikimate pathway can divert carbon to ccMA, a high value chemical. We transferred a ccMA-inducible transcription factor, CatM, from Acinetobacter baylyi ADP1 into C. glutamicum and screened a promoter library to isolate variants with high sensitivity and dynamic range to ccMA by providing benzoate, which is converted to ccMA intracellularly. The biosensor also detected exogenously supplied ccMA, suggesting the presence of a putative ccMA transporter in C. glutamicum, though the external ccMA concentration threshold to elicit a response was 100-fold higher than the concentration of benzoate required to do so through intracellular ccMA production. We then developed a chorismate biosensor, in which a chorismate inducible promoter regulated by natively expressed QsuR was optimized to exhibit a dose-dependent response to exogenously supplemented quinate (a chorismate precursor). A chorismate–pyruvate lyase encoding gene, ubiC, was introduced into C. glutamicum to lower the intracellular chorismate pool, which resulted in loss of dose dependence to quinate. Further, a knockout strain that blocked the conversion of quinate to chorismate also resulted in absence of dose dependence to quinate, validating that the chorismate biosensor is specific to intracellular chorismate pool. The ccMA and chorismate biosensors were dually inserted into C. glutamicum to simultaneously detect intracellularly produced chorismate and ccMA. Biosensors, such as those developed in this study, can be applied in C. glutamicum for multiplex sensing to expedite pathway design and optimization through metabolic engineering in this promising chassis organism. One-Sentence Summary High-throughput screening of promoter libraries in Corynebacterium glutamicum to establish transcription factor based biosensors for key metabolic intermediates in shikimate and β-ketoadipate pathways.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Overexpression of RuBisCO form I and II genes in Rhodopseudomonas palustris TIE-1 augments polyhydroxyalkanoate production heterotrophically and autotrophically

ABSTRACT With the rising demand for sustainable renewable resources, microorganisms capable of producing bioproducts such as bioplastics are attractive. While many bioproduction systems are well-studied in model organisms, investigating non-model organisms is essential to expand the field and utilize metabolically versatile strains. This investigation centers on Rhodopseudomonas palustris TIE-1, a purple non-sulfur bacterium capable of producing bioplastics. To increase bioplastic production, genes encoding the putative regulatory protein PhaR and the depolymerase PhaZ of the polyhydroxyalkanoate (PHA) biosynthesis pathway were deleted. Genes associated with pathways that might compete with PHA production, specifically those linked to glycogen production and nitrogen fixation, were deleted. Additionally, RuBisCO form I and II genes were integrated into TIE-1’s genome by a phage integration system, developed in this study. Our results show that deletion of phaR increases PHA production when TIE-1 is grown photoheterotrophically with butyrate and ammonium chloride (NH 4 Cl). Mutants unable to produce glycogen or fix nitrogen show increased PHA production under photoautotrophic growth with hydrogen and NH 4 Cl. The most significant increase in PHA production was observed when RuBisCO form I and form I & II genes were overexpressed, five times under photoheterotrophy with butyrate, two times with hydrogen and NH 4 Cl, and two times under photoelectrotrophic growth with N 2 . In summary, inserting copies of RuBisCO genes into the TIE-1 genome is a more effective strategy than deleting competing pathways to increase PHA production in TIE-1. The successful use of the phage integration system opens numerous opportunities for synthetic biology in TIE-1. IMPORTANCE Our planet has been burdened by pollution resulting from the extensive use of petroleum-derived plastics for the last few decades. Since the discovery of biodegradable plastic alternatives, concerted efforts have been made to enhance their bioproduction. The versatile microorganism Rhodopseudomonas palustris TIE-1 (TIE-1) stands out as a promising candidate for bioplastic synthesis, owing to its ability to use multiple electron sources, fix the greenhouse gas CO 2 , and use light as an energy source. Two categories of strains were meticulously designed from the TIE-1 wild-type to augment the production of polyhydroxyalkanoate (PHA), one such bioplastic produced. The first group includes mutants carrying a deletion of the phaR or phaZ genes in the PHA pathway, and those lacking potential competitive carbon and energy sinks to the PHA pathway (namely, glycogen biosynthesis and nitrogen fixation). The second group comprises TIE-1 strains that overexpress RuBisCO form I or form I & II genes inserted via a phage integration system. By studying numerous metabolic mutants and overexpression strains, we conclude that genetic modifications in the environmental microbe TIE-1 can improve PHA production. When combined with other approaches (such as reactor design, use of microbial consortia, and different feedstocks), genetic and metabolic manipulations of purple nonsulfur bacteria like TIE-1 are essential for replacing petroleum-derived plastics with biodegradable plastics like PHA.

Ranaivoarisoa, Tahina Onina↗
DOE OSTI2025

Modification and analysis of context-specific genome-scale metabolic models: methane-utilizing microbial chassis as a case study

ABSTRACT Context-specific genome-scale model (CS-GSM) reconstruction is becoming an efficient strategy for integrating and cross-comparing experimental multi-scale data to explore the relationship between cellular genotypes, facilitating fundamental or applied research discoveries. However, the application of CS modeling for non-conventional microbes is still challenging. Here, we present a graphical user interface that integrates COBRApy, EscherPy, and RIPTiDe, Python-based tools within the BioUML platform, and streamlines the reconstruction and interrogation of the CS genome-scale metabolic frameworks via Jupyter Notebook. The approach was tested using -omics data collected for Methylotuvimicrobium alcaliphilum 20Z R , a prominent microbial chassis for methane capturing and valorization. We optimized the previously reconstructed whole genome-scale metabolic network by adjusting the flux distribution using gene expression data. The outputs of the automatically reconstructed CS metabolic network were comparable to manually optimized i IA409 models for Ca-growth conditions. However, the CS model questions the reversibility of the phosphoketolase pathway and suggests higher flux via primary oxidation pathways. The model also highlighted unresolved carbon partitioning between assimilatory and catabolic pathways at the formaldehyde-formate node. Only a very few genes and only one enzyme with a predicted function in C1 metabolism, a homolog of the formaldehyde oxidation enzyme ( fae1-2 ), showed a significant change in expression in La-growth conditions. The CS-GSM predictions agreed with the experimental measurements under the assumption that the Fae1-2 is a part of the tetrahydrofolate-linked pathway. The cellular roles of the tungsten (W)-dependent formate dehydrogenase ( fdhAB ) and fae homologs ( fae1-2 and fae3 ) were investigated via mutagenesis. The phenotype of the f dhAB mutant followed the model prediction. Furthermore, a more significant reduction of the biomass yield was observed during growth in La-supplemented media, confirming a higher flux through formate. M. alcaliphilum 20Z R mutants lacking fae1-2 did not display any significant defects in methane or methanol-dependent growth. However, contrary to fae1, the fae1-2 homolog failed to restore the formaldehyde-activating enzyme function in complementation tests. Overall, the presented data suggest that the developed computational workflow supports the reconstruction and validation of CS-GSM networks of non-model microbes. IMPORTANCE The interrogation of various types of data is a routine strategy to explore the relationship between genotype and phenotype. An efficient approach for integrating and cross-comparing experimental multi-scale data in the context of whole-genome-based metabolic network reconstruction becomes a powerful tool that facilitates fundamental and applied research discoveries. The present study describes the reconstruction of a context-specific (CS) model for the methane-utilizing bacterium, Methylotuvimicrobium alcaliphilum 20Z R . M. alcaliphilum 20Z R is becoming an attractive microbial platform for the production of biofuels, chemicals, pharmaceuticals, and bio-sorbents for capturing atmospheric methane. We demonstrate that this pipeline can help reconstruct metabolic models that are similar to manually curated networks. Furthermore, the model is able to highlight previously overlooked pathways, thus advancing fundamental knowledge of non-model microbial systems or promoting their development toward biotechnological or environmental implementations.

Kulyashov, M. A.↗