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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 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Multiplex growth rate phenotyping of synthetic mutants in selection to engineer glucose and xylose co‐utilization in Escherichia coli

ABSTRACT Engineering the simultaneous consumption of glucose and xylose sugars is critical to enable the sustainable production of biofuels from lignocellulosic biomass. In most major industrial microorganisms glucose completely inhibits the uptake of xylose, limiting efficient sugar mixture conversion. In E . coli removal of the major glucose transporter PTS allows for glucose and xylose co‐consumption but only after prolonged adaptation, which is an effective process but hard to control and prone to co‐evolving undesired traits. Here we synthetically engineer mutants to target sugar co‐consumption properties; we subject a PTS − mutant to a short adaptive step and subsequently either delete or overexpress key genes previously suggested to affect sugar consumption. Screening the co‐consumption properties of these mutants individually is very laborious. We show we can evaluate sugar co‐consumption properties in parallel by culturing the mutants in selection and applying a novel approach that computes mutant growth rates in selection using chromosomal barcode counts obtained from Next‐Generation Sequencing. We validate this multiplex growth rate phenotyping approach with individual mutant pure cultures, identify new instances of mutants cross‐feeding on metabolic byproducts, and, importantly, find that the rates of glucose and xylose co‐consumption can be tuned by altering glucokinase expression in our PTS − background. Biotechnol. Bioeng. 2017;114: 885–893. © 2016 Wiley Periodicals, Inc.

Groot, Joost↗
DOE OSTI2022

Muconic acid production from glucose and xylose in Pseudomonas putida via evolution and metabolic engineering

Muconic acid is a bioprivileged molecule that can be converted into direct replacement chemicals for incumbent petrochemicals and performance-advantaged bioproducts. In this study, Pseudomonas putida KT2440 is engineered to convert glucose and xylose, the primary carbohydrates in lignocellulosic hydrolysates, to muconic acid using a model-guided strategy to maximize the theoretical yield. Using adaptive laboratory evolution (ALE) and metabolic engineering in a strain engineered to express the D-xylose isomerase pathway, we demonstrate that mutations in the heterologous D-xylose:H + symporter (XylE), increased expression of a major facilitator superfamily transporter (PP_2569), and overexpression of aroB encoding the native 3-dehydroquinate synthase, enable efficient muconic acid production from glucose and xylose simultaneously. Using the rationally engineered strain, we produce 33.7 g L -1 muconate at 0.18 g L -1 h -1 and a 46% molar yield (92% of the maximum theoretical yield). This engineering strategy is promising for the production of other shikimate pathway-derived compounds from lignocellulosic sugars.

09 BIOMASS FUELS↗
DOE OSTI2015

SnCl 4 -catalyzed isomerization/dehydration of xylose and glucose to furanics in water

A number of Lewis acid catalysts were screened for their effectiveness in converting both xylose and glucose in aqueous media to furfural and 5-HMF, respectively. While other catalysts were found to be more active, SnCl 4 was identified as the most selective Lewis acid. Hydrolysis of SnCl 4 was observed at various concentrations and temperatures resulting in the production of Brønsted acidic protons in a 3.5:1 ratio to Sn 4+ at all SnCl 4 concentrations above 60°C. As a consequence, there was no need to add a Brønsted acid in order to promote the dehydration of either xylose or glucose. SnCl 4 -promoted isomerization/dehydration of xylose and glucose at 140°C in water resulted in conversions of 55% and 33%, respectively, after 2 h of reaction, and furfural and 5-HMF selectivities of up to 58% and 27%, respectively. Significant conversion of sugars to humins was observed in both cases, and in the case of glucose, degradation of 5-HMF to levulinic and formic acids was also noted. The effects of secondary reactions could be greatly suppressed by extraction of the furanic product as it was produced. Here, using n-butanol as the extracting agent, xylose and glucose conversions of 90% and 75%, respectively, were observed after 5 h of reaction, and the selectivities to furfural and 5-HMF increased to 85% and 69%, respectively. Small additional increases in the furfural and 5-HMF selectivities were obtained by adding LiCl to the aqueous phase without much effect on the conversion of either sugar. In this case, the selectivities to furfural and 5-HMF were 88% and 72%, respectively, after 5 h of reaction at 140°C.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Data from Enhanced 2′-Fucosyllactose Production by Engineered Saccharomyces cerevisiae using Xylose as a Co-Substrate

2′-Fucosyllactose (2′-FL), a human milk oligosaccharide with confirmed benefits for infant health, is a promising infant formula ingredient. Although Escherichia coli , Saccharomyces cerevisiae , Corynebacterium glutamicum , and Bacillus subtilis have been engineered to produce 2′-FL, their titers and productivities need be improved for economic production. Glucose along with lactose have been used as substrates for producing 2′-FL, but accumulation of by-products due to overflow metabolism of glucose hampered efficient production of 2′-FL regardless of a host strain. To circumvent this problem, we used xylose, which is the second most abundant sugar in plant cell wall hydrolysates and is metabolized through oxidative metabolism, for the production of 2′-FL by engineered yeast. Specifically, we modified an engineered S. cerevisiae strain capable of assimilating xylose to produce 2′-FL from a mixture of xylose and lactose. First, a lactose transporter (Lac12) from Kluyveromyces lactis was introduced. Second, a heterologous 2′-FL biosynthetic pathway consisting of enzymes Gmd, WcaG, and WbgL from E. coli was introduced. Third, we adjusted expression levels of the heterologous genes to maximize 2′-FL production. The resulting engineered yeast produced 25.5 g/L of 2′-FL with a volumetric productivity of 0.35 g/L∙h in a fed-batch fermentation with lactose and xylose feeding to mitigate the glucose repression. Interestingly, the major location of produced 2′-FL by the engineered yeast can be changed using different culture media. While 72% of the produced 2′-FL was secreted when a complex medium was used, 82% of the produced 2′-FL remained inside the cells when a minimal medium was used. As yeast extract is already used as food and animal feed ingredients, 2′-FL enriched yeast extract can be produced cost-effectively using the 2′-FL-accumulating yeast cells.

Conversion↗
DOE OSTI2014

Kinetic features of xylan de-polymerization in production of xylose monomer and furfural during acid pretreatment for kenaf, forage sorghums and sunn hemp feedstocks

A kinetic study of acid pretreatment was conducted for sorghum non-brown mid rib (SNBMR) ( Sorghum bicolor L Moench ), sorghum-brown mid rib (SBMR), sunn hemp ( Crotalaria juncea L ) and kenaf ( Gossypiumhirsutum L ), focusing on rates of xylose monomer and furfural formation. The kinetics was investigated using two independent variables, reaction temperature (150 and 160°C) and acid concentration (1 and 2 wt%), with a constant dry biomass loading of 10 wt% and a treatment time up to 20 min while sampling the mixture every 2 min. The experimental data were fitted using a two-step kinetic model based on irreversible pseudo first order kinetics at each step. Varied kinetic orders on the acid concentration, ranging from 0.2 to >3, were observed for both xylose and furfural formation, the values depending on the feedstock. The crystallinity index of raw biomass was shown to be a major factor influencing the rate of both xylose and furfural formation. As a result, a positive correlation was observed between the activation energy and biomass crystallinity index for xylose formation.

09 BIOMASS FUELS↗
DOE OSTI2023

PKA regulatory subunit Bcy1 couples growth, lipid metabolism, and fermentation during anaerobic xylose growth in Saccharomyces cerevisiae

Past work from our lab, focused on engineering the budding yeast Saccharomyces cerevisiae for fermentation of the non-native pentose sugar xylose, discovered that hyperactivation of the RAS/Protein Kinase A (PKA) pathway was needed for rapid anaerobic xylose fermentation. Interestingly, the mechanism of PKA hyperactivation has a dramatic impact on growth and metabolism on xylose; deletion of the RAS inhibitor IRA2 permits rapid growth and fermentation, while deletion of the PKA regulatory subunit BCY1 allows for fermentation without growth on xylose. To understand how a single deletion in the PKA pathway can decouple growth and metabolism, we performed transcriptomic analysis of these strains, predicting that altered PKA activity would impact global gene expression and identify pathways important for growth and metabolism coordination.

Gasch, Audrey↗
DOE OSTI2013

Co-fermentation of glucose, xylose and/or cellobiose by yeast

Provided herein are methods of using yeast cells to produce ethanol by contacting a mixture comprising xylose with a Spathaspora yeast cell under conditions suitable to allow the yeast to ferment at least a portion of the xylose to ethanol. The methods allow for efficient ethanol production from hydrolysates derived from lignocellulosic material and sugar mixtures including at least xylose and glucose or xylose, glucose and cellobiose.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Structure-based protein engineering of bacterial β-xylosidase to increase the production yield of xylobiose from xylose

Highlights: • The crystal structures of β-xylosidase from Bacillus pumilus in complex with xylobiose were determined. • β-xylosidase was engineered to increase the yield of xylobiose based on the determined structures. • The protein engineering strategy used in this study could be applied within the same family of enzymes. Xylobiose consists of two molecules of xylose and has been highly recognized as a food supplement because it possesses high prebiotic functions. β-xylosidase exhibits enzymatic activity to hydrolyze xylobiose, and the enzyme can also catalyze the reverse reaction in the presence of high concentrations of xylose. Previously, β-xylosidase from Bacillus pumilus IPO (BpXynB), belonging to GH family 43, was employed to produce xylobiose from xylose. To improve the enzymatic efficiency, this study determined the high-resolution structure of BpXynB in a complex with xylobiose and engineered BpXynB based on the structures. The structure of BpXynB deciphered the residues involved in the recognition of the xylobiose. A site-directed mutation at the residue for xylobiose recognition increased the yield of xylobiose by 20% compared to a similar activity of the wild type enzyme. The complex structure of the mutant enzyme and xylobiose provided the structural basis for a higher yield of the engineered protein. This engineered enzyme would enable a higher economic production of xylobiose, and a similar engineering strategy could be applied within the same family of enzymes.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Advances in S. cerevisiae Engineering for Xylose Fermentation and Biofuel Production: Balancing Growth, Metabolism, and Defense

Genetically engineering microorganisms to produce chemicals has changed the industrialized world. The budding yeast Saccharomyces cerevisiae is frequently used in industry due to its genetic tractability and unique metabolic capabilities. S. cerevisiae has been engineered to produce novel compounds from diverse sugars found in lignocellulosic biomass, including pentose sugars, like xylose, not recognized by the organism. Engineering high flux toward novel compounds has proved to be more challenging than anticipated since simply introducing pathway components is often not enough. Several studies show that the rewiring of upstream signaling is required to direct products toward pathways of interest, but doing so can diminish stress tolerance, which is important in industrial conditions. As an example of these challenges, we reviewed S. cerevisiae engineering efforts, enabling anaerobic xylose fermentation as a model system and showcasing the regulatory interplay’s controlling growth, metabolism, and stress defense. Enabling xylose fermentation in S. cerevisiae requires the introduction of several key metabolic enzymes but also regulatory rewiring of three signaling pathways at the intersection of the growth and stress defense responses: the RAS/PKA, Snf1, and high osmolarity glycerol (HOG) pathways. The current studies reviewed here suggest the modulation of global signaling pathways should be adopted into biorefinery microbial engineering pipelines to increase efficient product yields.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

Shotgun proteomic monitoring of Clostridium acetobutylicum during stationary phase of butanol fermentation using xylose and comparison with the exponential phase

Economically viable production of solvents through acetone butanol ethanol (ABE) fermentation requires a detailed understanding of Clostridium acetobutylicum. This study focuses on the proteomic profiling of C. acetobutylicum ATCC 824 from the stationary phase of ABE fermentation using xylose and compares with the exponential growth by shotgun proteomics approach. Comparative proteomic analysis revealed 22.9% of the C. acetobutylicum genome and 18.6% was found to be common in both exponential and stationary phases. The proteomic profile of C. acetobutylicum changed during the ABE fermentation such that 17 proteins were significantly differentially expressed between the two phases. Specifically, the expression of five proteins namely, CAC2873, CAP0164, CAP0165, CAC3298, and CAC1742 involved in the solvent production pathway were found to be significantly lower in the stationary phase compared to the exponential growth. Similarly, the expression of fucose isomerase (CAC2610), xylulose kinase (CAC2612), and a putative uncharacterized protein (CAC2611) involved in the xylose utilization pathway were also significantly lower in the stationary phase. These findings provide an insight into the metabolic behavior of C. acetobutylicum between different phases of ABE fermentation using xylose.

Butanol ABE fermentation Clostridium↗
DOE OSTI2024

Self-Buffering system for Cost-Effective production of lactic acid from glucose and xylose using Acid-Tolerant Issatchenkia orientalis

This study presents a cost-effective strategy for producing organic acids from glucose and xylose using the acid- tolerant yeast, Issatchenkia orientalis. I. orientalis was engineered to produce lactic acid from xylose, and the resulting strain, SD108XL, successfully converted sorghum hydrolysates into lactic acid. In order to enable low- pH fermentation, a self-buffering strategy, where the lactic acid generated by the SD108XL strain during fermentation served as a buffer, was developed. As a result, the SD108 strain produced 67 g/L of lactic acid from 73 g/L of glucose and 40 g/L of xylose, simulating a sugar composition of sorghum biomass hydrolysates. Moreover, techno-economic analysis underscored the efficiency of the self-buffering strategy in streamlining the downstream process, thereby reducing production costs. These results demonstrate the potential of I. orientalis as a platform strain for the cost-effective production of organic acids from cellulosic hydrolysates.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

SAPO-34/5A Zeolite Bead Catalysts for Furan Production from Xylose and Glucose

SAPO-34 zeolite crystals were grown on zeolite 5A beads, characterized, and then utilized to produce furfural from xylose and 5-hydroxymethylfurfural (HMF) from glucose. The SAPO-34/5A bead catalysts resulted in moderate furfural and HMF yields of 45% from xylose and 20% from glucose (463 K; 3 h) and were easier to recover than the SAPO-34 powder catalyst. At 463 K, the SAPO-34/5A beads were more selective than 0.02 M sulfuric acid for producing HMF and, unlike the sulfuric acid system, no levulinic acid was formed. The SAPO-34/5A bead catalysts had no significant loss in activity after three rounds of recycle when water washed or heated overnight between reactions; however, the heat-treated beads did show signs of thermal stress after the second reuse. The SAPO-34/5A bead catalysts show promise for dehydration reactions to produce furfural and HMF from xylose and glucose, respectively, and adapting the catalyst and the support bead could lead to even higher selectivities and yields.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Man o' War Mutation in UDP-α-D-Xylose Synthase Favors the Abortive Catalytic Cycle and Uncovers a Latent Potential for Hexamer Formation

The man o’ war (mow) phenotype in zebrafish is characterized by severe craniofacial defects due to a missense mutation in UDP-α-D-xylose synthase (UXS), an essential enzyme in proteoglycan biosynthesis. The mow mutation is located in the UXS dimer interface ~16 Å away from the active site, suggesting an indirect effect on the enzyme mechanism. We have examined the structural and catalytic consequences of the mow mutation (R236H) in the soluble fragment of human UXS (hUXS), which shares 93% sequence identity with the zebrafish enzyme. In solution, hUXS dimers undergo a concentration-dependent association to form a tetramer. Sedimentation velocity studies show that the R236H substitution induces the formation of a new hexameric species. Using two new crystal structures of the hexamer, we show that R236H and R236A substitutions cause a local unfolding of the active site that allows for a rotation of the dimer interface necessary to form the hexamer. The disordered active sites in the R236H and R236A mutant constructs displace Y231, the essential acid/base catalyst in the UXS reaction mechanism. The loss of Y231 favors an abortive catalytic cycle in which the reaction intermediate, UDP-α-D-4-keto-xylose, is not reduced to the final product, UDP-α-D-xylose. Surprisingly, the mow-induced hexamer is almost identical to the hexamers formed by the deeply divergent UXS homologues from Staphylococcus aureus and Helicobacter pylori (21% and 16% sequence identity, respectively). The persistence of a latent hexamer-building interface in the human enzyme suggests that the ancestral UXS may have been a hexamer.

Polizzi, Samuel J.↗
DOE OSTI2016

Pervaporation-assisted catalytic conversion of xylose to furfural

Furfural produced from the biomass-derived xylose may serve as a platform molecule for sustainable fuel production. The Brønsted acid-catalyzed dehydration of xylose to furfural is plagued by side reactions that form a set of soluble and insoluble degradation products, collectively known as humins, which reduce the yield of furfural. The formation of humins can be minimized by removal of furfural, either by steam stripping or by liquid-liquid extraction (LLE). However, both these techniques are very costly. The goal of this study was to demonstrate the feasibility of using pervaporation, a membrane process, to remove furfural as it is produced. A laboratory-scale reactor/membrane system was designed, built, and tested for this purpose and its performance for furfural production was compared with that achieved by carrying out the reaction with and without furfural extraction by LLE. Furfural production assisted by pervaporation (with a commercially available membrane or a triblock copolymer membrane) or LLE produced comparable amounts of furfural, and more than could be achieved by reaction without extraction. A model of the reaction kinetics and the rate of furfural extraction was fit to the pervaporation- and LLE-assisted furfural production data and was used to predict the performances of these processes at near-complete xylose conversion. Here, pervaporation is shown to have two advantages over LLE: pervaporation extracts a greater fraction of the furfural produced and the furfural concentration in the permeate phase is significantly higher than that present in the extractant phase obtained by LLE. It is noted that further improvement in the separation of furfural from the aqueous phase where it is produced can be achieved by using a more-permeable, thinner pervaporation membrane of larger area, and by operating the membrane at the reaction temperature.

Wang, Alex↗
DOE OSTI2012

Inhibition of d-xylose isomerase by polyols: atomic details by joint X-ray/neutron crystallography

A joint X-ray/neutron structure of d-xylose isomerase in complex with the inhibitor sorbitol was determined at room temperature at an acidic pH of 5.9. Protonation of the O5 O atom of the sugar was directly observed in the nuclear density maps. Under acidic conditions sorbitol gains a water-mediated interaction with the enzyme active site, which may explain the increased potency of the inhibitor at low pH. d-Xylose isomerase (XI) converts the aldo-sugars xylose and glucose to their keto analogs xylulose and fructose, but is strongly inhibited by the polyols xylitol and sorbitol, especially at acidic pH. In order to understand the atomic details of polyol binding to the XI active site, a 2.0 Å resolution room-temperature joint X-ray/neutron structure of XI in complex with Ni{sup 2+} cofactors and sorbitol inhibitor at pH 5.9 and a room-temperature X-ray structure of XI containing Mg{sup 2+} ions and xylitol at the physiological pH of 7.7 were obtained. The protonation of oxygen O5 of the inhibitor, which was found to be deprotonated and negatively charged in previous structures of XI complexed with linear glucose and xylulose, was directly observed. The Ni{sup 2+} ions occupying the catalytic metal site (M2) were found at two locations, while Mg{sup 2+} in M2 is very mobile and has a high B factor. Under acidic conditions sorbitol gains a water-mediated interaction that connects its O1 hydroxyl to Asp257. This contact is not found in structures at basic pH. The new interaction that is formed may improve the binding of the inhibitor, providing an explanation for the increased affinity of the polyols for XI at low pH.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Data for Self-Buffering System for Cost-Effective Production of Lactic Acid from Glucose and Xylose Using Acid-Tolerant Issatchenkia orientalis

This study presents a cost-effective strategy for producing organic acids from glucose and xylose using the acid-tolerant yeast, Issatchenkia orientalis . I. orientalis was engineered to produce lactic acid from xylose, and the resulting strain, SD108XL, successfully converted sorghum hydrolysates into lactic acid. In order to enable low-pH fermentation, a self-buffering strategy, where the lactic acid generated by the SD108XL strain during fermentation served as a buffer, was developed. As a result, the SD108 strain produced 67 g/L of lactic acid from 73 g/L of glucose and 40 g/L of xylose, simulating a sugar composition of sorghum biomass hydrolysates. Moreover, techno-economic analysis underscored the efficiency of the self-buffering strategy in streamlining the downstream process, thereby reducing production costs. These results demonstrate the potential of I. orientalis as a platform strain for the cost-effective production of organic acids from cellulosic hydrolysates.

Conversion↗
DOE OSTI2016

Bypassing the Pentose Phosphate Pathway: Towards Modular Utilization of Xylose

The efficient use of hemicellulose in the plant cell wall is critical for the economic conversion of plant biomass to renewable fuels and chemicals. Previously, the yeast Saccharomyces cerevisiae has been engineered to convert the hemicellulose-derived pentose sugars xylose and arabinose to D-xylulose-5-phosphate for conversion via the pentose phosphate pathway (PPP). However, efficient pentose utilization requires PPP optimization and may interfere with its roles in NADPH and pentose production. Here, we developed an alternative xylose utilization pathway that largely bypasses the PPP. In the new pathway, D-xylulose is converted to D-xylulose-1-phosphate, a novel metabolite to S. cerevisiae, which is then cleaved to glycolaldehyde and dihydroxyacetone phosphate. This synthetic pathway served as a platform for the biosynthesis of ethanol and ethylene glycol. The use of D-xylulose-1-phosphate as an entry point for xylose metabolism opens the way for optimizing chemical conversion of pentose sugars in S. cerevisiae in a modular fashion.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Unearthing the ecology of soil microorganisms using a high resolution DNA-SIP approach to explore cellulose and xylose metabolism in soil

We explored microbial contributions to decomposition using a sophisticated approach to DNA Stable Isotope Probing (SIP). Our experiment evaluated the dynamics and ecological characteristics of functionally defined microbial groups that metabolize labile and structural C in soils. We added to soil a complex amendment representing plant derived organic matter substituted with either 13 C-xylose or 13 C-cellulose to represent labile and structural C pools derived from abundant components of plant biomass. We found evidence for 13 C-incorporation into DNA from 13 C-xylose and 13 C-cellulose in 49 and 63 operational taxonomic units (OTUs), respectively. The types of microorganisms that assimilated 13 C in the 13 C-xylose treatment changed over time being predominantly Firrnicutes at day 1 followed by Bacteroidetes at day 3 and then Actinobacteria at day 7. These 13 C-labeling dynamics suggest labile C traveled through different trophic levels. In contrast, microorganisms generally metabolized cellulose-C after 14 days and did not change to the same extent in phylogenetic composition over time. Furthermore, microorganisms that metabolized cellulose-C belonged to poorly characterized but cosmopolitan soil lineages including Verrucomicrobia , Chlorotlexi , and Planctomycetes .

16s ribosomal-rna↗