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

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At least 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

High Throughput expression and characterization of laccases in Saccharomyces cerevisiae [Poster]

We are working to generate fundamental understanding of enzymatic depolymerization of lignin and using this understanding to engineer mixtures of enzymes that catalyze the reactions necessary to efficiently depolymerize lignin into defined fragments. Over the years the enzymes involved in these processes have been difficult to study, because 1) the enzymes thought to be most important, fungal laccases and peroxidases, are very difficult to express in soluble, active form; 2) the full complement of required enzymes and whether or not they act synergistically is not known; 3) analysis of bond cleavage events is difficult due to the lack of analytical tools for measuring bond cleavage events in either polymeric lignin or model lignin-like compounds.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRSDate not supplied

Investigating Biological Responses to Space-like Radiation using the yeast Saccharomyces cerevisiae

As we plan crewed missions to the Moon, Mars, and beyond, it is essential to understand how persistent exposure to space radiation affects biology. Unlike on the International Space Station, where crew support and sample return are possible, experiments for long-duration missions require autonomous systems with no sample return. Human cells would be ideal biosensors, but limitations in culture methods, extended prelaunch storage, and long flight durations make it very difficult to keep human cells alive. Unlike other model systems, yeast can survive the constraints of long-duration spaceflight. Despite a billion years of evolution separating yeast from humans, we share homology in hundreds of genes important for basic cell function, including responses to DNA damage. Thus, yeast are excellent biosensors for detecting types/extent of damage induced by space radiation. BioSentinel is NASA’s latest biological CubeSat, and first interplanetary space bioscience mission. BioSentinel is manifested on Artemis 1, the first test flight of NASA’s Space Launch System, in the coming year. The BioSensor payload within BioSentinel contains two yeast strains. The wild type serves as a control for health and “normal” DNA damage repair (DDR). The rad51 deletion mutant is defective for DDR and will undergo alterations to growth and metabolism as it accumulates radiation damage. Changes in growth and metabolic activity will be measured using a 3-color LED detection system and the metabolic redox dye alamarBlue®. Preliminary tests indicate a significant change in alamarBlue response to space-like, low-dose ionizing radiation. We will discuss these findings in four parts – Introduction to biological CubeSats and the BioSentinel mission (presented by Sergio Santa Maria), preliminary responses to space-like ionizing radiation (presented here), a deeper dive into tracking metabolic changes after exposure to ionizing radiation (presented by Diana Gentry), and a look into methods for correcting flight optical data (presented by Abbey Kim). This work is funded by NASA’s Advanced Exploration Systems.

CubeSat↗
NASA NTRS2015

Perchlorate Reduction by Yeast for Mars Exploration

Martian soil contains high levels (0.6 percentage by mass) of calcium perchlorate (Ca(ClO4)2), which readily dissociates into calcium and the perchlorate ion (ClO4−) in water. Even in trace amounts, perchlorates are toxic to humans and have been implicated in thyroid dysfunction. Devising methods to lessen perchlorate contamination is crucial to minimizing the health risks associated with human exploration and colonization of Mars. We designed a perchlorate reduction pathway, which sequentially reduces perchlorate to chloride (Cl−) and oxygen (O2), for implementation in the yeast Saccharomyces cerevisiae. Using genes obtained from perchlorate reducing bacteria Azospira oryzae and Dechloromonas aromatica, we plan to assemble this pathway directly within S. cerevisiae through recombinational cloning. A perchlorate reduction pathway would enable S. cerevisiae to lower perchlorate levels and produce oxygen, which may be harvested or used directly by S. cerevisiae for aerobic growth and compound synthesis. Moreover, using perchlorate as an external electron acceptor could improve the efficiency of redox-imbalanced production pathways in yeast. Although several perchlorate reducing bacteria have been identified and utilized in water treatment systems on Earth, the widespread use of S. cerevisiae as a synthetic biology platform justifies the development of a perchlorate reducing strain for implementation on Mars.

Perchlorate↗
DOE OSTI2024

Oxygenation influences xylose fermentation and gene expression in the yeast genera Spathaspora and Scheffersomyces

Abstract Background Cost-effective production of biofuels from lignocellulose requires the fermentation of d -xylose. Many yeast species within and closely related to the genera Spathaspora and Scheffersomyces (both of the order Serinales) natively assimilate and ferment xylose. Other species consume xylose inefficiently, leading to extracellular accumulation of xylitol. Xylitol excretion is thought to be due to the different cofactor requirements of the first two steps of xylose metabolism. Xylose reductase (XR) generally uses NADPH to reduce xylose to xylitol, while xylitol dehydrogenase (XDH) generally uses NAD + to oxidize xylitol to xylulose, creating an imbalanced redox pathway. This imbalance is thought to be particularly consequential in hypoxic or anoxic environments. Results We screened the growth of xylose-fermenting yeast species in high and moderate aeration and identified both ethanol producers and xylitol producers. Selected species were further characterized for their XR and XDH cofactor preferences by enzyme assays and gene expression patterns by RNA-Seq. Our data revealed that xylose metabolism is more redox balanced in some species, but it is strongly affected by oxygen levels. Under high aeration, most species switched from ethanol production to xylitol accumulation, despite the availability of ample oxygen to accept electrons from NADH. This switch was followed by decreases in enzyme activity and the expression of genes related to xylose metabolism, suggesting that bottlenecks in xylose fermentation are not always due to cofactor preferences. Finally, we expressed XYL genes from multiple Scheffersomyces species in a strain of Saccharomyces cerevisiae . Recombinant S. cerevisiae expressing XYL1 from Scheffersomyces xylosifermentans , which encodes an XR without a cofactor preference, showed improved anaerobic growth on xylose as the primary carbon source compared to S. cerevisiae strain expressing XYL genes from Scheffersomyces stipitis . Conclusion Collectively, our data do not support the hypothesis that xylitol accumulation occurs primarily due to differences in cofactor preferences between xylose reductase and xylitol dehydrogenase; instead, gene expression plays a major role in response to oxygen levels. We have also identified the yeast Sc. xylosifermentans as a potential source for genes that can be engineered into S. cerevisiae to improve xylose fermentation and biofuel production.

09 BIOMASS FUELS↗
DOE OSTI2026

Data for Resourceful and Economical Designing of Fermentation Medium for Lab and Commercial Strains of Yeast from Alternative Feedstock: Transgenic Oilcane

Sugarcane plant engineered to accumulate lipids in its vegetative tissue is being developed as a new bioenergy crop. The new crop would be a source of juice, oil, and cellulosic sugars. However, limited tolerance of industrially recognized yeasts towards inhibitors generated during the processing of lignocellulosic biomass to produce fermentable sugars is a major challenge in developing scalable processes for second-generation drop-in fuel production. To this end, hydrolysates generated from engineered sugarcane—‘oilcane’ bagasse contain added phenolics and fatty acids that further restrict the growth of fermenting microorganisms and necessitate nutrient supplementation and/or detoxification of hydrolysate which makes the fermentation process expensive. Herein, we propose a resourceful and economical approach for growing lab and commercial strains of S. cerevisiae on unrefined cellulosic sugars aerobically and fermentatively. An equal ratio of hydrolysate and juice was found optimum for growth and fermentation by lab and commercial strains of Saccharomyces cerevisiae engineered for xylose fermentation. The industrial strain grew and fermented efficiently under low aeration conditions having an ethanol titer, yield, specific and volumetric productivities of 46.96 ± 0.19 g/l, 0.51 ± 0.00 g/g, 0.27 ± 0.02 g/g.h and 1.95 ± 0.01 g/l.h, respectively, while the lab strain grew better under higher aeration conditions having the ethanol titer, yield, specific and volumetric productivities of 24.93 ± 0.09, 0.27 ± 0.00 g/g, 0.17 ± 0.00 g/g.h and 1.04 ± 0.00 g/l.h, respectively. Acclimation of cultures in a blended medium significantly improved the performance of the yeast strains. The addition of transgenic oilcane juice, which is inedible and rich in amino acids, to the hydrolysate averted the need for expensive nutrient supplementation and detoxification steps of hydrolysate. The approach provides an economical solution to reduce the cost of fermentation at an industrial scale for second-generation drop-in fuel production.

Biomass Analytics↗
NASA NTRS2017

Development of Storage Methods for Saccharomyces Strains to be Utilized for In situ Nutrient Production in Long-Duration Space Missions

Long-duration space missions will benefit from closed-loop life support technologies that minimize mass, volume, and power as well as decrease reliance on Earth-based resupply. A system for In situ production of essential vitamins and nutrients can address the documented problem of degradation of stored food and supplements. Research has shown that the edible yeast Saccharomyces cerevisiae can be used as an on-demand system for the production of various compounds that are beneficial to human health. A critical objective in the development of this approach for long-duration space missions is the effective storage of the selected microorganisms. This research investigates the effects of different storage methods on survival rates of the non-sporulating probiotic S. boulardii, and S. cerevisiae spores and vegetative cells. Dehydration has been shown to increase long-term yeast viability, which also allows increased shelf-life and reduction in mass and volume. The process of dehydration causes detrimental effects on vegetative cells, including oxidative damage and membrane disruption. To maximize cell viability, various dehydration methods are tested here, including lyophilization (freeze-drying), air drying, and dehydration by vacuum. As a potential solution to damage caused by lyophilization, the efficacy of various cryoprotectants was tested. Furthermore, in an attempt to maintain higher survival rates, the effect of temperature during long-term storage was investigated. Data show spores of the wild-type strain to be more resilient to dehydration-related stressors than vegetative cells of either strain, and maintain high viability rates even after one year at room temperature. In the event that engineering the organism to produce targeted nutrient compounds interferes with effective sporulation of S. cerevisiae, a more robust method for improving vegetative cell storage is being sought. Therefore, anhydrobiotic engineering of S. cerevisiae and S. boulardii is being conducted

nutrient↗
NASA NTRS2017

Development of Storage Methods for Saccharomyces Strains to be Utilized for In Situ Nutrient Production in Long-Duration Space Missions

Long-duration space missions will benefit from closed-loop life support technologies that minimize mass, volume, and power as well as decrease reliance on Earth-based resupply. A system for In situ production of essential vitamins and nutrients can address the documented problem of degradation of stored food and supplements. Research has shown that the edible yeast Saccharomyces cerevisiae can be used as an on-demand system for the production of various compounds that are beneficial to human health. A critical objective in the development of this approach for long-duration space missions is the effective storage of the selected microorganisms. This research investigates the effects of different storage methods on survival rates of the non-sporulating probiotic S. boulardii, and S. cerevisiae spores and vegetative cells. Dehydration has been shown to increase long-term yeast viability, which also allows increased shelf-life and reduction in mass and volume. The process of dehydration causes detrimental effects on vegetative cells, including oxidative damage and membrane disruption. To maximize cell viability, various dehydration methods are tested here, including lyophilization (freeze-drying), air drying, and dehydration by vacuum. As a potential solution to damage caused by lyophilization, the efficacy of various cryoprotectants was tested. Furthermore, in an attempt to maintain higher survival rates, the effect of temperature during long-term storage was investigated. Data show spores of the wild-type strain to be more resilient to dehydration-related stressors than vegetative cells of either strain, and maintain high viability rates even after one year at room temperature. In the event that engineering the organism to produce targeted nutrient compounds interferes with effective sporulation of S. cerevisiae, a more robust method for improving vegetative cell storage is being sought. Therefore, anhydrobiotic engineering of S. cerevisiae and S. boulardii is being conducted.

life support↗
DOE OSTI2023

Risk Assessment of Industrial Microbes Using a Terrestrial Mesocosm Platform

Abstract Industrial microbes and bio-derived products have emerged as an integral component of the bioeconomy, with an array of agricultural, bioenergy, and biomedical applications. However, the rapid development of microbial biotechnology raises concerns related to environmental escape of laboratory microbes, detection and tracking thereof, and resultant impact upon native ecosystems. Indeed, though wild-type and genetically modified microbes are actively deployed in industrial bioprocesses, an understanding of microbial interactivity and impact upon the environment is severely lacking. In particular, the persistence and sustained ecosystem impact of industrial microbes following laboratory release or unintentional laboratory escape remains largely unexplored. Herein, we investigate the applicability of soil-sorghum mesocosms for the ecological risk assessment of the industrial microbe, Saccharomyces cerevisiae . We developed and applied a suite of diagnostic and bioinformatic analyses, including digital droplet PCR, microscopy, and phylogenomic analyses to assess the impacts of a terrestrial ecosystem perturbation event over a 30-day time course. The platform enables reproducible, high-sensitivity tracking of S. cerevisiae in a complex soil microbiome and analysis of the impact upon abiotic soil characteristics and soil microbiome population dynamics and diversity. The resultant data indicate that even though S. cerevisiae is relatively short-lived in the soil, a single perturbation event can have sustained impact upon mesocosm soil composition and underlying microbial populations in our system, underscoring the necessity for more comprehensive risk assessment and development of mitigation and biocontainment strategies in industrial bioprocesses.

09 BIOMASS FUELS↗
DOE OSTI2020

Rewiring yeast metabolism to synthesize products beyond ethanol

Saccharomyces cerevisiae, Baker's yeast, is the industrial workhorse for producing ethanol and the subject of substantial metabolic engineering research in both industry and academia. S. cerevisiae has been used to demonstrate production of a wide range of chemical products from glucose. However, in many cases, the demonstrations report titers and yields that fall below thresholds for industrial feasibility. Ethanol synthesis is a central part of S. cerevisiae metabolism, and redirecting flux to other products remains a barrier to industrialize strains for producing other molecules. Furthermore, removing ethanol producing pathways leads to poor fitness, such as impaired growth on glucose. Here, we review metabolic engineering efforts aimed at restoring growth in non-ethanol producing strains with emphasis on relieving glucose repression associated with the Crabtree effect and rewiring metabolism to provide access to critical cellular building blocks. Finally, substantial progress has been made in the past decade, but many opportunities for improvement remain.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

All You Can Eat Yeast: Substituting Hexose Transporters With AtSWEET7 Alleviates Glucose Repression, Enabling Simultaneous Utilization of Sugars in Renewable Feedstocks

Yeast sugar transporters have highly evolved for preferential glucose transport, a significant roadblock for utilizing non-glucose sugars in renewable feedstocks such as lignocellulosic biomass. To enable simultaneous transport of multiple sugars, native hexose transporters were replaced by SWEET7p from Arabidopsis thaliana in engineered Saccharomyces cerevisiae capable of fermenting xylose. Engineered S. cerevisiae exhibited reduced glucose preference, simultaneously co-fermenting glucose, mannose, fructose, and xylose both in synthetic and industrial media. Continuous culture experiments demonstrated the co-consuming phenotype and alleviation of glucose repression by engineered S. cerevisiae. In addition to hexose and pentose, the NKSW7-1 strain consumed xylitol as a carbon source. Through transcriptomic and metabolomic analysis of the NKSW7-1 strain, we show that the replacement of HXT1-7 with AtSWEET7 led to systemwide reprogramming of the central carbon metabolism. This broad transport capacity of AtSWEET7p holds promise for achieving co-consumption of all sugars in underutilized renewable feedstocks by microbial cell factory.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Metabolic flux and resource balance in the oleaginous yeast Rhodotorula toruloides

The yeast Rhodotorula toruloides is a promising bioproduction organism due to its high lipid yields and ability to grow on cheap and abundant substrates. Quantitative, systems-level assessment of its metabolic activity is accordingly merited. Resource-balance analysis (RBA) models capture not only reaction stoichiometry but also enzyme requirements for catalysis, providing valuable tools for understanding metabolic trade-offs and optimizing metabolic engineering strategies. Here, in this work, we present systems-level measurements of R. toruloides metabolic flux based on isotope tracing and metabolic flux analysis. In combination with new proteomic measurements, these flux data are used to parameterize a genome-scale resource balance model rtRBA. We find that S. cerevisiae and R. toruloides grow at nearly indistinguishable rates using similar biosynthetic but dramatically different central metabolic programs. R. toruloides consumes one-fifth as much glucose, which it metabolizes primarily via the pentose phosphate pathway and TCA cycle unlike primarily glycolysis in S. cerevisiae . Overall, across these two divergent yeasts, protein abundances aligned more closely than metabolic flux. Resource balance modeling of these metabolic programs predicts superior theoretical yields but lower productivities in R. toruloides than S. cerevisiae for industrial chemicals, highlighting the value of rapid glucose uptake for productivity but respiratory metabolism for yields.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

Leveraging 13C-Labeling to Assign Molecular Formulas to Unknown Yeast Metabolites

Mass spectrometry analyses have identified tens of thousands of unknown small molecule-associated peaks in different biological specimens. Notably, even the simplest and best studied organisms like Escherichia coli and Saccharomyces cerevisiae yield thousands of unknown peaks. A key question is how many of these reflect actual novel endogenous metabolites. To explore this, Mahieu and Patti used complete 13 C -labeling in E. coli to credential peaks as biological. This reduced the number of unknowns by more than 90%. Here, we carry out similar uniform 13 C-labeling in the Baker’s yeast S. cerevisiae and two less-studied bioenergy-relevant yeasts Rhodotorula toruloides (lipid producer) and Issatchenkia orientalis (organic acid producer). Identification of unknown metabolite peaks and their molecular formulas is facilitated through software tailored for 13 C labeling data and resulting knowledge of carbon atom count. A classification model evaluates the plausibility of each candidate formula, with peaks lacking plausible candidate formulas unlikely to reflect metabolite molecular ions. This approach prioritizes about one hundred candidate abundant unknown metabolites with logical molecular formulas. Most of these are species-specific rather than conserved across yeasts, and more are found in the nonmodel yeasts than S. cerevisiae. Thus, 13 C-labeling data on unknown metabolites highlights the potential for discovering new metabolites and pathways in nonmodel yeasts.

Carbon↗
DOE OSTI2025

Structural basis for sensitivity and acquired resistance of fungal cap guanine-N7 methyltransferases to the antifungal antibiotic sinefungin

Abstract The essential enzyme messenger RNA (mRNA) (guanine-N7) methyltransferase catalyzes S-adenosylmethionine (SAM)-dependent conversion of GpppRNA ends to the m7GpppRNA cap structure characteristic of eukaryal mRNAs. The antibiotic sinefungin (SFG) is a SAM analog in which the S-CH3 sulfonium moiety of SAM is replaced by a C-NH2 amine. Available evidence indicates that the antifungal activity of SFG is exerted via inhibition of fungal cap methyltransferase Abd1. Here we report that recombinant Kluyveromyces lactis and Saccharomyces cerevisiae Abd1 are 240-fold and 485-fold more sensitive to inhibition by SFG than by the reaction product S-adenosylhomocysteine (SAH). Crystal structures of K. lactis and S. cerevisiae Abd1 as binary complexes with SAH or SFG and ternary complexes with GTP•SFG highlight how SFG makes two hydrogen bonds from its C-NH2 amine to the guanine-O6 and -N7 atoms of GTP that account for its higher affinity vis-à-vis SAH and SAM. Through a genetic screen to isolate SFG-resistant S. cerevisiae strains, a conserved tyrosine (Tyr416) that interacts with the cap guanine in Abd1 was identified as a key determinant of SFG potency. Tyr416 Abd1 variants confer SFG resistance in vitro by weakening cap-assisted SFG interactions with Abd1. Our study illuminates the basis for the exquisite SFG sensitivity of fungal cap methyltransferases.

Biochemistry & Molecular Biology↗
DOE OSTI2021

raogroupuiuc/scer_ure2

Data repository for the S. cerevisiae ure2 deletion project Project: Investigating the role of the transcriptional regulator Ure2 on the metabolism of Saccharomyces cerevisiae: a multi-omics approach. Key points • Deletion of URE2 increases ethanol and lipid production in Saccharomyces cerevisiae. • Deletion of URE2 reduces glycogen and trehalose production. • Metabolic changes mimic nitrogen starvation and autophagic response.

Deewan, Anshu↗
DOE OSTI2024

Lulabcodes/Coarse-grained_Sc_Model

This repository contains the source code for the coarse-grained, systemic, and dynamic model of Saccharomyces cerevisiae. Related publishments: Emergence of Orchestrated and Dynamic Metabolism of Saccharomyces cerevisiae. Coarse-Grained Modeling Elucidates Differential Metabolism of Saccharomyces cerevisiae under Varied Nutrient Limitations.

Lai, Yi-Hui (Cindy)↗