Engineering oleaginous yeast for versatile production of fuels and bioproducts
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Liu, Di [Sandia National Laboratories (SNL-CA), Li↗
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Machine Learning-Guided Design of Perovskite Oxides for High-Temperature Oxygen Sensing
Presentation slides for 2025 MRS Fall Meeting & Exhibit. Reliable oxygen sensors are vital for high temperature applications including combustion engines, steel production, and petrochemical refining, yet identifying stable, high-performance materials for such environments remain challenge. We apply machine learning (ML) to predict the atmospheric oxygen partial pressure–dependent conductivity of perovskite oxides, combining data from the Materials Project and published datasets.
high temperature gas sensor↗
Engineering carbon conserving microbes for production of industrial chemicals from lignocellulosic biomass-derived C5 sugars
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09 BIOMASS FUELS↗
Engineering an increase in ethanol production by altering cofactor specificity
The present invention provides for the manipulation of cofactor usage in a recombinant host cell to increase the formation of desirable products. In some embodiments, the invention provides for a recombinant microorganism comprising a mutation in one or more native enzymes such that their cofactor specificity is altered in such a way that overall cofactor usage in the cell is balanced for a specified pathway and there is an increase in a specific product formation within the cell. In some embodiments, endogenous enzymes are replaced by enzymes with an alternate cofactor specificity from a different species.
09 BIOMASS FUELS↗
Moving Forward Together: How a Software Engineering Department Can Impact Developer Productivity in a Research Organization.
Abstract not provided.
Willenbring, James Michael↗
Isolated oleaginous yeast
Some aspects provide engineered microbes for oil production. Methods for microbe engineering and for use of engineered microbes are also provided herein. Such engineered microbes exhibit greatly enhanced conversion yields and TAG synthesis and storage properties.
Stephanopoulos, Gregory↗
Growth-uncoupled propanediol production in a Thermoanaerobacterium thermosaccharolyticum strain engineered for high ethanol yield
Abstract Cocultures of engineered thermophilic bacteria can ferment lignocellulose without costly pretreatment or added enzymes, an ability that can be exploited for low cost biofuel production from renewable feedstocks. The hemicellulose-fermenting species Thermoanaerobacterium thermosaccharolyticum was engineered for high ethanol yield, but we found that the strains switched from growth-coupled production of ethanol to growth uncoupled production of acetate and 1,2-propanediol upon growth cessation, producing up to 6.7 g/L 1,2-propanediol from 60 g/L cellobiose. The unique capability of this species to make 1,2-propanediol from sugars was described decades ago, but the genes responsible were not identified. Here we deleted genes encoding methylglyoxal reductase, methylglyoxal synthase and glycerol dehydrogenase. Deletion of the latter two genes eliminated propanediol production. To understand how carbon flux is redirected in this species, we hypothesized that high ATP levels during growth cessation downregulate the activity of alcohol and aldehyde dehydrogenase activities. Measurements with cell free extracts show approximately twofold and tenfold inhibition of these activities by 10 mM ATP, supporting the hypothesized mechanism of metabolic redirection. This result may have implications for efforts to direct and maximize flux through alcohol dehydrogenase in other species.
09 BIOMASS FUELS↗
Sustainable production of 2,3,5,6-Tetramethylpyrazine at high titer in engineered Corynebacterium glutamicum
The industrial amino acid production workhorse, Corynebacterium glutamicum naturally produces low levels of 2,3,5,6-tetramethylpyrazine (TMP), a valuable flavor, fragrance, and commodity chemical. Here, we demonstrate TMP production (~0.8 g L –1 ) in C. glutamicum type strain ATCC13032 via overexpression of acetolactate synthase and/or α-acetolactate decarboxylase from Lactococcus lactis in CGXII minimal medium supplemented with 40 g L –1 glucose. This engineered strain also demonstrated growth and TMP production when the minimal medium was supplemented with up to 40% (v v –1 ) hydrolysates derived from ionic liquid-pretreated sorghum biomass. Further, a key objective was to take the fully engineered strain developed in this study and interrogate medium parameters that influence the production of TMP, a critical post-strain engineering optimization. Design of experiments in a high-throughput plate format identified glucose, urea, and their ratio as significant components affecting TMP production. These two components were further optimized using response surface methodology. In the optimized CGXII medium, the engineered strain could produce up to 3.56 g L –1 TMP (4-fold enhancement in titers and 2-fold enhancement in yield, mol mol –1 ) from 80 g L –1 glucose and 11.9 g L –1 urea in shake flask batch cultivation.
59 BASIC BIOLOGICAL SCIENCES↗
Engineering of increased L-Threonine production in bacteria by combinatorial cloning and machine learning
The goal of this study is to develop a general strategy for bacterial engineering using an integrated synthetic biology and machine learning (ML) approach. This strategy was developed in the context of increasing L-threonine production in Escherichia coli ATCC 21277. A set of 16 genes was initially selected based on metabolic pathway relevance to threonine biosynthesis and used for combinatorial cloning to construct a set of 385 strains to generate training data (i.e., a range of L-threonine titers linked to each of the specific gene combinations). Hybrid (regression/classification) deep learning (DL) models were developed and used to predict additional gene combinations in subsequent rounds of combinatorial cloning for increased L-threonine production based on the training data. As a result, E. coli strains built after just three rounds of iterative combinatorial cloning and model prediction generated higher L-threonine titers (from 2.7 g/L to 8.4 g/L) than those of patented L-threonine strains being used as controls (4-5 g/L). Interesting combinations of genes in L-threonine production included deletions of the tdh, metL, dapA, and dhaM genes as well as overexpression of the pntAB, ppc, and aspC genes. Mechanistic analysis of the metabolic system constraints for the best performing constructs offers ways to improve the models by adjusting weights for specific gene combinations. Graph theory analysis of pairwise gene modifications and corresponding levels of L-threonine production also suggests additional rules that can be incorporated into future ML models.
60 APPLIED LIFE SCIENCES↗
Engineering Perovskite Precursor Inks for Scalable Production of High‐Efficiency Perovskite Photovoltaic Modules
Abstract Blade coating of perovskite solar cells (PSCs) and modules has progressed considerably toward the industrial production of perovskite photovoltaics. Developing stable perovskite precursors is critical for achieving uniform coating over large areas. Here, the engineering of a perovskite precursor solution consisting of 2‐methoxyethanol (2‐Me) and 1,3‐dimethyl‐imidazolidinone (DMI) with superior intermediate phase stability that enables scalable production of efficient perovskite solar modules is reported. With this perovskite precursor solution, uniform and pinhole‐less perovskite film is deposited over a large area of > 100 cm 2 and higher‐efficiency PSCs and modules are obtained. The best‐performing unit cell and module with n‐i‐p configuration reach power conversion efficiencies of 23.4% and 20.1%, respectively. Additionally, a series of non‐destructive metrology methods, such as spectroscopic ellipsometry, hyperspectral photoluminescence, electroluminescence, and laser beam‐induced current mapping, are employed to assess and guide the development the blade‐coated perovskite modules. This results show that rational engineering of precursor inks for blade coating is promising for the scalable production of efficient perovskite solar modules.
36 MATERIALS SCIENCE↗
Engineering robust microorganisms for organic acid production
Abstract Organic acids are an important class of compounds that can be produced by microbial conversion of renewable feedstocks and have huge demands and broad applications in food, chemical, and pharmaceutical industries. An economically viable fermentation process for production of organic acids requires robust microbial cell factories with excellent tolerance to low pH conditions, high concentrations of organic acids, and lignocellulosic inhibitors. In this review, we summarize various strategies to engineer robust microorganisms for organic acid production and highlight their applications in a few recent examples.
59 BASIC BIOLOGICAL SCIENCES↗
Engineering Clostridium cellulovorans for highly selective n ‐butanol production from cellulose in consolidated bioprocessing
Abstract Cellulosic n ‐butanol from renewable lignocellulosic biomass has gained increased interest. Previously, we have engineered Clostridium cellulovorans , a cellulolytic acidogen, to overexpress the bifunctional butyraldehyde/butanol dehydrogenase gene adh E2 from C. acetobutylicum for n ‐butanol production from crystalline cellulose. However, butanol production by this engineered strain had a relatively low yield of approximately 0.22 g/g cellulose due to the coproduction of ethanol and acids. We hypothesized that strengthening the carbon flux through the central butyryl‐CoA biosynthesis pathway and increasing intracellular NADH availability in C. cellulovorans adh E2 would enhance n ‐butanol production. In this study, thiolase ( thl A CA ) from C. acetobutylicum and 3‐hydroxybutyryl‐CoA dehydrogenase ( hbd CT ) from C. tyrobutyricum were overexpressed in C. cellulovorans adh E2 to increase the flux from acetyl‐CoA to butyryl‐CoA. In addition, ferredoxin‐NAD(P) + oxidoreductase ( fnr ), which can regenerate the intracellular NAD(P)H and thus increase butanol biosynthesis, was also overexpressed. Metabolic flux analyses showed that mutants overexpressing these genes had a significantly increased carbon flux toward butyryl‐CoA, which resulted in increased production of butyrate and butanol. The addition of methyl viologen as an electron carrier in batch fermentation further directed more carbon flux towards n ‐butanol biosynthesis due to increased reducing equivalent or NADH. The engineered strain C. cellulovorans adh E2‐ fnr CA ‐ thl A CA ‐ hbd CT produced n ‐butanol from cellulose at a 50% higher yield (0.34 g/g), the highest ever obtained in batch fermentation by any known bacterial strain. The engineered C. cellulovorans is thus a promising host for n ‐butanol production from cellulosic biomass in consolidated bioprocessing.
Bao, Teng↗
Systems Engineering of Rhodococcus opacus to Enable Production of Drop-in Fuels from Lignocellulose
Production of drop-in fuels from lignocellulose using Rhodococcus opacus PD630 (hereafter R. opacus) is a challenging goal. During the grant period we have pushed the field forward significantly in several areas of research. Towards the end goal of accelerating the adoption of R. opacus in biofuel production, during the grant period we have expanded the phenotypic characterization of R. opacus grown in single aromatic (model lignocellulosic) compounds or their mixtures, modeling the growth conditions in lignocellulosic biomass. Harnessing the power of adaptive evolution, we produced evolved R. opacus isolates with superior lignin valorization capabilities and identified differentially expressed genes and pathways after adaptation. We used next generation multi-omic techniques such as genomic, transcriptomic, and metabolomic analyses, to identify the catabolic pathways used by R. opacus to degrade aromatic compounds and funnel these degradation products into central metabolism, as well as the aromatic transport genes required for increased tolerance and utilization. Taking this information one step further, we identified endogenous transcription factors and regulatory mechanisms important for degradation of five model aromatic compounds. To accurately estimate R. opacus growth and consumption on model lignin compounds we pioneered the use of novel extraction procedures prior to GC-MS analysis. Alongside 13 C-metabolic flux analysis, we have elucidated the metabolic routes preferred by Rhodococcus opacus during aromatic compound degradation. Finally, we used in tandem lipidomics and high-resolution mass spectrometry to identify the modulation of mycolic acids and phospholipid membrane composition modification as a strategy for aromatic tolerance in R. opacus. Being a non-model organism, R. opacus lacks the breadth of tools and technical foundation which drive biofuel research in more well-understood microbes such as Escherichia coli. To reduce this burden for use, we designed and produced new tools for genomic manipulation and engineering in R. opacus. These engineering breakthroughs support efficient genomic editing, enabling gene overexpression, repression, and genetic alteration. Using these tools, we have generated synthetically engineered strains with increased lipogenesis and growth, both positive traits required for increased lignin valorization. Optimizing engineered strains for biofuel production from lignocellulose requires extremely sophisticated synthetic rewiring of metabolism. To facilitate systems-level reorganization of metabolism in R. opacus, we created a genome-scale model that accurately predicts metabolic flux and growth rates on the aromatic compound phenol. Lignin requires extensive pre-treatment before biological degradation by R. opacus. Towards an eventual goal of degrading real-world lignin, we developed new depolymerization processes to generate lignin breakdown products (LBP). We optimized LBP storage and composition analysis techniques, enabling accurate prediction of specific LBP compound integration into cell wall components. Overall, through the work funded by this grant we generated 20 manuscripts (17 published, 3 in review/preparation), methods for increased accuracy in metabolomics of aromatic compounds, multiple genetic tools for altering the R. opacus genome, genome scale models for predicting flux through metabolic pathways, as well as multi-omic data for community use. The work funded by this grant has increased the knowledge of aromatic degradation in bacteria and advanced our efforts to optimize R. opacus for lignin valorization.
09 BIOMASS FUELS↗
Alternatives to MARVEL Power Conversion -- Comparison of Stirling Engine Thermal Efficiency and Design to Other Power Conversion Cycles
PRESENTATION for CONFERENCE PAPER: The Microreactor Applications, Research, Validation, and Evaluation (MARVEL) Reactor is a small liquid-metal thermal reactor that will be built at the Idaho National Laboratory to demonstrate design and operating processes for microreactors, microgrid integration, and process heat applications. Power conversion in the MARVEL design is provided by Stirling engines, which have disadvantages in nuclear environments. Compared to Stirling engine performance, some alternative power cycles can increase power production when coupled to a liquid-metal thermal reactor. In this paper, the thermal efficiency of MARVEL’s power production with Stirling engines is compared to the thermal efficiency of power production with MARVEL and alternative power cycles. Those cycles include a superheated Rankine cycle, open and closed Brayton cycles, and a supercritical carbon dioxide cycle. All cycles (except the Stirling engines) were modeled with an intermediate helium loop to meet MARVEL’s principal design criteria. All models are simple designs with conservative assumptions for consistent comparison. Detailed optimization will depend largely on reactor location and application, and the relative merit of each cycle is discussed for different environmental conditions. The study informs significant early decisions on power cycle design and economics for deployment of advanced microreactors as they move from theory and concept to execution.
21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
Alternatives to MARVEL Power Conversion – Comparison of Stirling Engine Thermal Efficiency and Design to other Power Conversion Cycles
The Microreactor Applications, Research, Validation, and Evaluation (MARVEL) Reactor is a small liquid-metal thermal reactor that will be built at the Idaho National Laboratory to demonstrate design and operating processes for microreactors, microgrid integration, and process heat applications. Power conversion in the MARVEL design is provided by Stirling engines, which have disadvantages in nuclear environments. Compared to Stirling engine performance, some alternative power cycles can increase power production when coupled to a liquid-metal thermal reactor In this paper, the thermal efficiency of MARVEL’s power production with Stirling engines is compared to the thermal efficiency of power production with MARVEL and alternative power cycles. Those cycles include a superheated Rankine cycle, open and closed Brayton cycles, and a supercritical carbon dioxide cycle. All cycles (except the Stirling engines) were modeled with an intermediate helium loop to meet MARVEL’s principal design criteria. All models are simple designs with conservative assumptions for consistent comparison. Detailed optimization will depend largely on reactor location and application, and the relative merit of each cycle is discussed for different environmental conditions. The study informs significant early decisions on power cycle design and economic
21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
Further engineering of R. toruloides for the production of terpenes from lignocellulosic biomass
Abstract Background Mitigation of climate change requires that new routes for the production of fuels and chemicals be as oil-independent as possible. The microbial conversion of lignocellulosic feedstocks into terpene-based biofuels and bioproducts represents one such route. This work builds upon previous demonstrations that the single-celled carotenogenic basidiomycete, Rhodosporidium toruloides , is a promising host for the production of terpenes from lignocellulosic hydrolysates. Results This study focuses on the optimization of production of the monoterpene 1,8-cineole and the sesquiterpene α-bisabolene in R. toruloides . The α-bisabolene titer attained in R. toruloides was found to be proportional to the copy number of the bisabolene synthase (BIS) expression cassette, which in turn influenced the expression level of several native mevalonate pathway genes. The addition of more copies of BIS under a stronger promoter resulted in production of α-bisabolene at 2.2 g/L from lignocellulosic hydrolysate in a 2-L fermenter. Production of 1,8-cineole was found to be limited by availability of the precursor geranylgeranyl pyrophosphate (GPP) and expression of an appropriate GPP synthase increased the monoterpene titer fourfold to 143 mg/L at bench scale. Targeted mevalonate pathway metabolite analysis suggested that 3-hydroxy-3-methyl-glutaryl-coenzyme A reductase (HMGR), mevalonate kinase (MK) and phosphomevalonate kinase (PMK) may be pathway bottlenecks are were therefore selected as targets for overexpression. Expression of HMGR, MK, and PMK orthologs and growth in an optimized lignocellulosic hydrolysate medium increased the 1,8-cineole titer an additional tenfold to 1.4 g/L. Expression of the same mevalonate pathway genes did not have as large an impact on α-bisabolene production, although the final titer was higher at 2.6 g/L. Furthermore, mevalonate pathway intermediates accumulated in the mevalonate-engineered strains, suggesting room for further improvement. Conclusions This work brings R. toruloides closer to being able to make industrially relevant quantities of terpene from lignocellulosic biomass.
09 BIOMASS FUELS↗
Regulatory response to a hybrid ancestral nitrogenase in Azotobacter vinelandii
Biological nitrogen fixation, the microbial reduction of atmospheric nitrogen to bioavailable ammonia, represents both a major limitation on biological productivity and a highly desirable engineering target for synthetic biology. However, the engineering of nitrogen fixation requires an integrated understanding of how the gene regulatory dynamics of host diazotrophs respond across sequence-function space of its central catalytic metalloenzyme, nitrogenase. Here, we interrogate this relationship by analyzing the transcriptome of Azotobacter vinelandii engineered with a phylogenetically inferred ancestral nitrogenase protein variant. The engineered strain exhibits reduced cellular nitrogenase activity but recovers wild-type growth rates following an extended lag period. We find that expression of genes within the immediate nitrogen fixation network is resilient to the introduced nitrogenase sequence-level perturbations. Rather the sustained physiological compatibility with the ancestral nitrogenase variant is accompanied by reduced expression of genes that support trace metal and electron resource allocation to nitrogenase. Our results spotlight gene expression changes in cellular processes adjacent to nitrogen fixation as productive engineering considerations to improve compatibility between remodeled nitrogenase proteins and engineered host diazotrophs.
59 BASIC BIOLOGICAL SCIENCES↗
Exogenous electricity flowing through cyanobacterial photosystem I drives CO 2 valorization with high energy efficiency
Nature's biocatalytic processes are driven by photosynthesis, whereby photosystems I and II are connected in series for light-stimulated generation of fuel products or electricity. Externally supplying electricity directly to the photosynthetic electron transfer chain (PETC) has numerous potential benefits, although strategies for achieving this goal have remained elusive. Here we report an integrated photo-electrochemical architecture which shuttles electrons directly to PETC in living cyanobacteria. The cathode of this architecture electrochemically interfaces with cyanobacterial cells that have a lack of photosystem II activity and cannot perform photosynthesis independently. Illumination of the cathode channels electrons from an external circuit to intracellular PETC through photosystem I, ultimately fueling cyanobacterial conversion of CO 2 into acetate. We observed acetate formation when supplying both illumination and exogenous electrons under intermittent conditions (e.g., in a 30 s supply plus 30 min interval condition of both light and exogenous electrons). The energy conversion efficiency for acetate production under programmed intermittent LED illumination (400–700 nm) and exogenous electron supply reached ca. 9%, when taking into account the number of photons and electrons received by the biotic system, and ca. 3% for total photons and electrons supplied to the cyanobacteria. This approach is applicable for generating various CO 2 reduction products by using engineered cyanobacteria, one of which has enabled electrophototrophic production of ethylene, a broadly used hydrocarbon in the chemical industry. The resulting bio-electrochemical hybrid has the potential to produce fuel chemicals with numerous potential advantages over standalone natural and artificial photosynthetic approaches.
54 ENVIRONMENTAL SCIENCES↗