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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

A transcriptomic atlas of acute stress response to low pH in multiple Issatchenkia orientalis strains

Because of its natural stress tolerance to low pH, Issatchenkia orientalis (a.k.a. Pichia kudriavzevii) is a promising non-model yeast for bio-based production of organic acids. Yet, this organism is relatively unstudied, and specific mechanisms of its tolerance to low pH are poorly understood, limiting commercial use. In this study, we selected 12 I. orientalis strains with varying acid stress tolerance (six tolerant and six susceptible) and profiled their transcriptomes in different pH conditions to study potential mechanisms of pH tolerance in this species. We identified hundreds of genes whose expression response is shared by tolerant strains but not by susceptible strains, or vice versa, as well as genes whose responses are reversed between tolerant and susceptible strains. We mapped regulatory mechanisms of transcriptomic responses via motif analysis as well as differential network reconstruction, identifying several transcription factors, including Stb5, Mac1, and Rtg1/Rtg3, some of which are known for their roles in acid response in Saccharomyces cerevisiae. Functional genomics analysis of short-listed genes and transcription factors suggested significant roles for energy metabolism and translation-related processes, as well as the cell wall integrity pathway and RTG-dependent retrograde signaling pathway. Finally, we conducted additional experiments for two organic acids, 3-hydroxypropionate and citramalate, to eliminate acid-specific effects and found potential roles for glycolysis and trehalose biosynthesis specifically for response to low pH. In summary, our approach of comparative transcriptomics and phenotypic contrasting, along with a multi-pronged bioinformatics analysis, suggests specific mechanisms of tolerance to low pH in I. orientalis that merit further validation through experimental perturbation and engineering.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Data for A Transcriptomic Atlas of Acute Stress Response to Low pH in Multiple Issatchenkia orientalis Strains

Because of its natural stress tolerance to low pH, Issatchenkia orientalis (a.k.a. Pichia kudriavzevii ) is a promising non-model yeast for bio-based production of organic acids. Yet, this organism is relatively unstudied, and specific mechanisms of its tolerance to low pH are poorly understood, limiting commercial use. In this study, we selected 12 I. orientalis strains with varying acid stress tolerance (six tolerant and six susceptible) and profiled their transcriptomes in different pH conditions to study potential mechanisms of pH tolerance in this species. We identified hundreds of genes whose expression response is shared by tolerant strains but not by susceptible strains, or vice versa, as well as genes whose responses are reversed between tolerant and susceptible strains. We mapped regulatory mechanisms of transcriptomic responses via motif analysis as well as differential network reconstruction, identifying several transcription factors, including Stb5, Mac1, and Rtg1/Rtg3, some of which are known for their roles in acid response in Saccharomyces cerevisiae . Functional genomics analysis of short-listed genes and transcription factors suggested significant roles for energy metabolism and translation-related processes, as well as the cell wall integrity pathway and RTG-dependent retrograde signaling pathway. Finally, we conducted additional experiments for two organic acids, 3-hydroxypropionate and citramalate, to eliminate acid-specific effects and found potential roles for glycolysis and trehalose biosynthesis specifically for response to low pH. In summary, our approach of comparative transcriptomics and phenotypic contrasting, along with a multi-pronged bioinformatics analysis, suggests specific mechanisms of tolerance to low pH in I. orientalis that merit further validation through experimental perturbation and engineering.

Conversion↗
DOE OSTI2026

Influence of Inorganic Carbon Sources on Low-pH Succinic Acid Production by Issatchenkia orientalis : Process Insights and Kinetic Analysis

Bio-based succinic acid (SA) production has attracted significant interest; however, the relationship between fermentation conditions and SA biosynthesis remains insufficiently understood, particularly under low-pH operation. In this study, an engineered, acid-tolerant, nonmodel yeast, Issatchenkia orientalis , was employed to investigate the role of inorganic carbon supplementation in SA production from glucose. Because regulation of gas-phase CO 2 during fermentation is challenging due to low solubility and off-gas losses, liquid-phase inorganic carbon sources, carbonic acid (H 2 CO 3 ) and sodium carbonate (Na 2 CO 3 ), were evaluated as indirect CO 2 donors. Fermentations were conducted in a corn steep liquor-based medium under acidic conditions. Shake-flask experiments demonstrated that H 2 CO 3 supplementation increased SA production, achieving a maximum titer of 8.9 g/L and a yield of 0.46 g/g glucose. Kinetic analysis of bench-scale fermentations showed that the SA formation was well described by the Luedeking–Piret model, indicating mixed growth-associated product formation with a substantial nongrowth-associated contribution under carbonic acid supplementation. Guided by these kinetic insights, a two-stage fed-batch fermentation strategy was implemented, resulting in an SA titer of 30 g/L and a yield of 0.57 g/g glucose within 115 h. Overall, this work provides process-relevant insights into integrating inorganic carbon utilization with low-pH fermentation to inform more sustainable SA biomanufacturing.

fed-batch fermentation↗
DOE OSTI2023

Metabolic engineering of low-pH-tolerant non-model yeast, Issatchenkia orientalis , for production of citramalate

Methyl methacrylate (MMA) is an important petrochemical with many applications. However, its manufacture has a large environmental footprint. Combined biological and chemical synthesis (semisynthesis) may be a promising alternative to reduce both cost and environmental impact, but strains that can produce the MMA precursor (citramalate) at low pH are required. A non-conventional yeast, Issatchenkia orientalis, may prove ideal, as it can survive extremely low pH. Here, we demonstrate the engineering of I. orientalis for citramalate pro- duction. Using sequence similarity network analysis and subsequent DNA synthesis, we selected a more active citramalate synthase gene (cimA) variant for expression in I. orientalis. We then adapted a piggyBac transposon system for I. orientalis that allowed us to simultaneously explore the effects of different cimA gene copy numbers and integration locations. A batch fermentation showed the genome-integrated-cimA strains produced 2.0 g/L citramalate in 48 h and a yield of up to 7% mol citramalate/mol consumed glucose. These results demonstrate the potential of I. orientalis as a chassis for citramalate production.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Data for Metabolic Engineering of Low-pH-Tolerant Non-Model Yeast, Issatchenkia orientalis , for Production of Citramalate

Methyl methacrylate (MMA) is an important petrochemical with many applications. However, its manufacture has a large environmental footprint. Combined biological and chemical synthesis (semisynthesis) may be a promising alternative to reduce both cost and environmental impact, but strains that can produce the MMA precursor (citramalate) at low pH are required. A non-conventional yeast, Issatchenkia orientalis , may prove ideal, as it can survive extremely low pH. Here, we demonstrate the engineering of I. orientalis for citramalate production. Using sequence similarity network analysis and subsequent DNA synthesis, we selected a more active citramalate synthase gene (cimA) variant for expression in I. orientalis . We then adapted a piggyBac transposon system for I. orientalis that allowed us to simultaneously explore the effects of different cimA gene copy numbers and integration locations. A batch fermentation showed the genome-integrated-cimA strains produced 2.0 g/L citramalate in 48 h and a yield of up to 7% mol citramalate/mol consumed glucose. These results demonstrate the potential of I. orientalis as a chassis for citramalate production.

Conversion↗
DOE OSTI2025

Mixed lipid bilayers enable enhanced stability and activity retention of Lipase A in low-pH environments

Lipase A (LipA) from Bacillus subtilis is a versatile and industrially relevant enzyme, but its activity is compromised under acidic conditions due to aggregation and deactivation. In this study, we investigated the use of mixed lipid bilayers to stabilize and improve activity retention of LipA at low pH. Attachment to lipid bilayers, particularly those containing cationic lipids, greatly enhanced the long-term stability of LipA in acidic conditions while also leading to improvements in activity. Tethering to cationic bilayers not only shifted the apparent pH activity profile toward more acidic conditions, but also significantly enhanced activity retention upon incubation at pH 6. Notably, this protective effect persisted even without direct tethering, indicating that reversible, non-covalent interactions with the bilayer surface are sufficient for long-term stability. Circular dichroism further revealed that the secondary structure of LipA was retained, while dynamic light scattering suggested that activity loss in solution was primarily due to aggregation of the native state. Together, these findings support a model in which lipid bilayers mitigate aggregation and stabilize LipA through transient interactions and electrostatic modulation of the local surface environment. Furthermore, this approach exemplifies a simple, tether-free strategy for enhancing enzyme performance in acidic or destabilizing conditions, with implications for biocatalysis, biosensing, and therapeutic delivery.

Biocatalysis↗
DOE OSTI2024

Low pH Titanium Electrochemistry in the Presence of Sulfuric Acid and its Implications for Redox Flow Battery Applications

Titanium (Ti) is a promising elemental redox active species for redox flow batteries (RFBs) due to its 100x availability in the Earth crust, and 10x lower cost (compared to elemental vanadium). Furthermore, Ti salts are highly soluble in water and concentrations >5 M can be easily obtained. Seeking to harness the higher solubility (and hence energy density) of the Ti electrolyte for flow battery applications, the Ti 4+ /Ti 3+ redox couple was investigated at high concentrations (up to 5 M) relevant to RFB applications. The behavior of Ti ions in H 2 SO 4 supported electrolytes was investigated by varying the ratio of Ti redox active species to counterion. The electrochemical characteristics, transport properties, and redox kinetics of the Ti 4+ /Ti 3+ redox couple were measured and the impact of the Ti x+ to solvating ligand ratio was examined. The coordination structures around solvated Ti x+ ions were spectroscopically determined and the effect of solvation structure on the Ti 3+ /Ti 4+ redox rate constants were examined and correlated to the calculated solvation energy (hence distinguishing between inner- and outer-sphere processes) and the role of catalysts was addressed. The Ti electrolyte development guidelines presented herein will advance the development of Ti-based RFBs as a promising pathway towards cost effective, grid-scale energy storage.

Electrochemistry↗
DOE OSTI2023

129 I, 99 Tc, And U Distribution Coefficients of Subsurface Sediments Collected from the Proposed Site of the Environmental Management Disposal Facility

Performance Assessment calculations were completed in 2020 to evaluate the Environmental Management Disposal Facility (EMDF), a proposed new low-level radioactive waste (LLW) disposal facility on the U.S. Department of Energy’s Oak Ridge Reservation (ORR). Among the large number of input parameters needed for such calculations, are distribution coefficients (K d values; radionuclide concentration solid:liquid ratio) that provide a measure of the tendency of radionuclides to bind to sediments. The objective of this study was to measure K d values of three radionuclides that may pose a disproportionately large amount of risk, U, 129 I and 99 Tc. The average I K d value for the 14 geological materials recovered from the proposed EMDF site was 37.8 mL/g and ranged from -1.8 to 140.9 mL/g. These values were consistent, but somewhat larger than previous measurements made with ORR sediments and were about an order of magnitude greater than those used in previous EMDF PA calculations. The median Tc K d value was 365.7 mL/g, much greater than previously reported using ORR geological materials. Five of the 14 tested geological materials sorbed large quantities of Tc, suggesting that the weakly sorbing Tc(VII) species had been reduced to the sparingly soluble Tc(IV) species. The five strongly sorbing sediments had apparent Tc solubility values of approximately <10 -8 mol/L. The median U K d value was 5,726 mL/g. All of the tested geological materials had large K d values, ranging from 625 to >10,208 mL/g. Among the sediment samples that exhibited strong U binding, the apparent solubility value was approximately <10 -9 mol/L. Based on sediment properties and general ORR geological considerations, it was proposed that much of the I and Tc retention could be attributed to the site materials exhibiting low pH (average pH = 4.94), low redox status, and/or the elevated levels of iron oxides, manganese oxides, and natural organic matter. Similarly, the extremely high U binding measured in these sediments may also be attributed to the low conditions of carbonates, which can complex and therefore solubilize uranyl in these tests due to the low pH, and also the relatively high concentrations of iron and organic coatings on these samples. An implication of this study is that the areas of the EMDF subsurface environment may have natural properties for attenuating I, Tc, and U movement, and potentially other radionuclides, thereby possibly reducing risk posed by burial of LLW at this site. This document is a revision of SRNL-STI-2021-00404, Revision 0 that includes new data describing U K d values and new I and Tc K d values for four Nolichucky sediments. These new results were integrated into the data presented in the original document.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
NASA NTRS1991

Growth and maintenance of an embryogenic cell culture of daylily (Hemerocallis) on hormone-free medium

Callus cultures of the diploid daylily (Hemerocallis) clone Autumn Blaze' were initiated and maintained in hormone-containing nutrient medium. At various times (from 6 weeks to 1 year) after being initiated, hormone-derived cultures were evaluated for their ability to be maintained and to multiply on hormone-free medium at low pH (between pH 4 and 4.5). Cultures had to be exposed to hormone-containing medium for at least 12 weeks before they could be maintained on hormone-free medium at low pH. The transition to maintainability on low pH hormone-free medium included the production of many aberrant embryonal forms ( neomorphs'). However, all hormone-derived cultures tested consisted entirely of preglobular stage proembryos (PGSPs) after 12-24 weeks on low pH hormone-free medium. PGSP cultures have been maintained and multiplied as such for over 1 year on low pH hormone-free medium. PGSPs continue their development into various somatic embryo stages when cultured on hormone-free medium buffered at pH 5.8. The production of well-formed somatic embryos was greatly enhanced when PGSPs were plated on activated charcoal impregnated filter papers that were placed on top of the agar surface. The gross morphology and histology of the PGSPs and stages of somatic embryo development are presented. The work shows that the ability of hormone-free medium at low pH to permit PGSP multiplication without development into later stages of embryo development is not restricted to carrot.

Non-NASA Center↗
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↗
NASA NTRS2006

In-Situ and Experimental Evidence for Acidic Weathering of Rocks and Soils on Mars

Experimental data for alteration of synthetic Martian basalts at pH=0-1 indicate that chemical fractionations at low pH are vastly different from those observed during terrestrial weathering. Rock analyses from Gusev crater are well described by the relationships apparent from low pH experimental alteration data. A model for rock surface alteration is developed which indicates that a leached alteration zone is present on rock surfaces at Gusev. This zone is not chemically fractionated to a large degree from the underlying rock interior, indicating that the rock surface alteration process has occurred at low fluid-to-rock ratio. The geochemistry of natural rock surfaces analyzed by APXS is consistent with a mixture between adhering soil/dust and the leached alteration zone. The chemistry of rock surfaces analyzed after brushing with the RAT is largely representative of the leached alteration zone. The chemistry of rock surfaces analyzed after grinding with the RAT is largely representative of the interior of the rock, relatively unaffected by the alteration process occurring at the rock surface. Elemental measurements from the Spirit, Opportunity, Pathfinder and Viking 1 landing sites indicate that soil chemistry from widely separated locations is consistent with the low-pH, low fluid to rock ratio alteration relationships developed for Gusev rocks. Soils are affected principally by mobility of FeO and MgO, consistent with alteration of olivine-bearing basalt and subsequent precipitation of FeO and MgO bearing secondary minerals as the primary control on soil geochemistry.

Hurowitz, J. A.↗
NASA NTRS1990

Low external pH replaces 2,4-D in maintaining and multiplying 2,4-D-initiated embryogenic cells of carrot

A mixed culture comprised of both embryonic globules and nonembryogenic callus was derived from seedling hypocotyls of Daucus carota cv. Scarlet Nantes on 2,4-D- containing medium using well-established methods. Then the mixed cultures were transferred to, and serially subcultured on, a hormone-free medium near pH 4. The medium contained 1 mM NH4+ as the sole nitrogen source. When cultured in this way, embryonic globules were able to multiply without development into later embryo stages. Nonembryogenic callus did not survive. Continuous culture of embryonic globules on this low pH hormone-free medium yielded cultures consisting entirely of preglobular stage proembryos (PGSPs). PGSP cultures have been maintained as such with continuous multiplication for nearly 2 years without loss of embryogenic potential. These hormone-free-maintained PGSPs continue their development to later embryo stages when cultured on the same hormone-free medium buffered at pH 5.8. We show that hormone-free medium near pH 4 can replace 2,4-D in its ability to sustain multiplication of 2,4-D-initiated embryogenic cells of carrot at an acceptable growth rate without their development into later embryo stages. This procedure provides selective conditions that do not permit the growth of non-embryogenic cells while providing an adequate environment for embryogenic cell proliferation and should prove invaluable in studying habituation.

Non-NASA Center↗
DOE OSTI2024

Water acidification aggravates lithium-induced toxicity represented by energy supply, oxidative stress, and cell fate in Daphnia magna neonates

Lithium is extensively utilized in industrial energy production, particularly in lithium-ion batteries, and in pharmaceuticals for the treating clinical mood disorders. Consequently, lithium is frequently detected in various environmental matrices. It has been reported to cause a range of toxic effects on aquatic organisms including oxidative stress, neurological disorders, and reproductive suppression. Water acidification is a global issue with numerous negative impacts on aquatic organisms. It can alter the physio-chemical properties and bioavailability of metal ions. The acidic leaching process during lithium battery treatment and global water acidification both suggest that lithium contamination often occurs in acidic environments. In the present study, Daphnia magna neonates were exposed to four treatments (control, lithium alone, low pH, and combined) to investigate whether an acidic environment exacerbates the toxic effects of lithium on aquatic organisms and to explore potential toxic action mechanisms. The results indicated that low pH posed a significant threat to the growth and reproduction of D. magna. When exposed to both lithium and low pH, there was increased lithium accumulation and an energy trade-off response, leading to increased energy allocation to reproduction and reduced energy for growth. Lithium exposure stimulated D. magna activity, while low pH inhibited it, suggesting that an imbalance in energy consumption and supply. Combined exposure to lithium and low pH resulted in severe oxidative stress due to mitochondrial dysfunction, under-utilization of energy substances, and increased ionic homeostasis disturbances. Consequently, the exposed organism altered apoptosis and autophagy processes to maintain homeostasis. In conclusion, the present study demonstrated that lithium and water acidification posed a population-level threat to D. magna, and their combined exposure significantly largely exacerbated the toxic effects.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗
DOE OSTI2021

129 I and 99 Tc Distribution Coefficients of Subsurface Sediments Collected from the Proposed Site of the Environmental Manage Disposal Facility

Performance Assessment calculations are presently underway to evaluate the Environmental Management Disposal Facility (EMDF), a proposed new low-level radioactive waste (LLW) disposal facility on the U.S. Department of Energy’s Oak Ridge Reservation (ORR). Among the large number of input parameters needed for such calculations, are distribution coefficients (K d values; radionuclide concentration solid:liquid ratio) that provide a measure of the tendency of radionuclides to bind to sediments. The objective of this study was to measure K d values of two radionuclides that may pose a disproportionately large amount of risk, 129 I and 99 Tc. The average I K d value for the 10 geological materials recovered from the proposed EMDF site was 52.3 mL/g and ranged from 2.7 to 140.9 mL/g. These values were consistent, but somewhat larger than previous measurements made with ORR sediments and were about an order of magnitude greater than those used in previous EMDF PA calculations. The median Tc K d value was 807.2 mL/g, much greater than previously reported using ORR geological materials. Five of the ten tested geological materials sorbed large quantities of Tc, suggesting that the weakly sorbing Tc(VII) species had been reduced to the very strongly binding and sparingly soluble Tc(IV) species. The five strongly sorbing sediment had apparent solubility values of approximately <10 -8 mol/L. Based on sediment properties and general ORR geological considerations, it was proposed that much of the I and Tc sorption could be attributed to the low pH (average pH = 4.94), low redox status, and/or the elevated levels of iron oxides, manganese oxides, and natural organic matter. An implication of this study is that the areas of the EMDF subsurface environment may have natural properties for attenuating I and Tc movement, thereby potentially reducing risk posed by burial of LLW at this site.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2026

Data for An End-to-End Pipeline for Succinic Acid Production at an Industrially Relevant Scale Using Issatchenkia orientalis

Microbial production of succinic acid (SA) at an industrially relevant scale has been hindered by high downstream processing costs arising from neutral pH fermentation for over three decades. Here, we metabolically engineer the acid-tolerant yeast Issatchenkia orientalis for SA production, attaining the highest titers in sugar-based media at low pH (pH 3) in fed-batch fermentations, i.e. 109.5 g/L in minimal medium and 104.6 g/L in sugarcane juice medium. We further perform batch fermentation using sugarcane juice medium in a pilot-scale fermenter (300×) and achieve 63.1 g/L of SA, which can be directly crystallized with a yield of 64.0%. Finally, we simulate an end-to-end low-pH SA production pipeline, and techno-economic analysis and life cycle assessment indicate our process is financially viable and can reduce greenhouse gas emissions by 34–90% relative to fossil-based production processes. We expect I. orientalis can serve as a general industrial platform for production of organic acids.

Metabolomics↗
DOE OSTI2026

Xylose metabolic engineering of Issatchenkia orientalis for 3-hydroxypropionic acid production from cellulosic hydrolysate without nutrient supplementation

Bioconversion of lignocellulosic biomass offers a promising alternative to petroleum-based chemical production. However, inefficient xylose utilization and toxic compounds in cellulosic hydrolysate limit microbial fermentation, as the hydrolysate contains substantial amounts of xylose in addition to glucose. To address these challenges, we engineered Issatchenkia orientalis to produce 3-hydroxypropionic acid (3-HP) directly from sorghum hydrolysate under low-pH conditions. A heterologous xylose utilization pathway consisting of XYL1, XYL2, and XYL3 from Scheffersomyces stipitis was introduced into an engineered 3-HP producing strain, enabling efficient conversion of xylose to 3-HP. The engineered strain produced 46.8 g/L 3-HP from sorghum hydrolysate without nutrient supplementation. To eliminate the lag phase under low-pH conditions, fermentation was conducted at pH 6.0 for the first three days, after which pH control was discontinued and in situ 3-HP accumulation buffered the culture. This partial pH control strategy increased 3-HP productivity by 55% from 0.20 to 0.31 g/L∙h, while maintaining low-pH conditions. Introducing an additional copy of XYL2 further increased 3-HP titer to 53.5 g/L and the yield by 33%, from 0.30 to 0.40 g/g sugars, with pH reaching 4.5 at the end of fermentation. This represents one of the highest reported 3-HP titers and yields from cellulosic hydrolysate without additional nutrient supplementation. This work demonstrates a nutrient-independent and low-pH bioprocess for upgrading lignocellulosic hydrolysate into 3-HP, highlighting the industrial potential of engineered xylose-utilizing I. orientalis for sustainable production of platform chemicals from renewable feedstocks.

3-Hydroxypropionic acid↗