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At least 469 records · Page 26
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Methods to Activate and Elucidate Complex Endogenous Sugar Metabolism in Yarrowia lipolytica

Yarrowia lipolytica has endogenous metabolism to use complex sugars derived from lignocellulosic biomass. However, many of these pathways are cryptic and hence either inactive or inefficient for xylose, arabinose, and cellobiose assimilation. Furthermore, we present collective methods to activate and elucidate these endogenous sugar pathways by performing short-term growth adaptation, determining the pathway efficiency, and conducting transcriptomic, enzymatic, and metabolic analyses to identify rate limiting steps for enhanced sugar consumption.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Chapter 3: New Developments on Ionic Liquid-Tolerant Microorganisms Leading Toward a More Sustainable Biorefinery

The growing concerns about climate change and energy security are driving the development of bio-based technologies to produce renewable liquid fuels and chemicals. Ionic liquids (ILs) have demonstrated to be promising solvents to pretreat lignocellulosic residues, promoting efficient enzymatic hydrolysis of lignocellulosic carbohydrates into sugars, which can be further used by microorganisms to produce biofuels and other value-added chemicals. Despite their unique properties to effectively deconstruct plant cell walls, ILs show strong interactions with the pretreated biomass, and their presence is often inhibitory to cellulolytic enzymes and microorganisms. The most advanced biorefinery concepts based on IL pretreatments focus on the development of more biocompatible ILs and more robust microbial strains with higher tolerance to ILs. This chapter provides an overview and a discussion over the main efforts performed on the screening and development of IL-tolerant microbial strains, as well as in more biocompatible IL pretreatment methods. These early research advancements in this field offer a baseline and a platform for future research with the goal of improving the sustainability and economic viability of IL pretreatment-based biorefineries.

bioconversion↗
DOE OSTI2021

High-Biomass Sorghums as a Feedstock for Renewable Fuels and Chemicals

High-biomass sorghums are intended for use in biorefineries that convert vegetative biomass into renewable fuels and chemicals. The majority of plant biomass consists of cell walls, a complex matrix of cellulose, hemicellulosic polysaccharides and lignin. In the biorefinery, the biomass is ground and then subjected to a thermo-chemical pretreatment (elevated temperature, high pressure, chemical catalysts) that disrupts the cell wall matrix and solubilizes some of the cell wall polymers, followed by enzymatic saccharification of the cellulose, which produces D-glucose. The glucose and sometimes also the xylose derived from the hydrolysis of the hemicellulosic polysaccharides, are subsequently converted to fuels or other useful chemicals by microbial biocatalysts. The genetic improvement of high-biomass sorghums has as its ultimate goals to maximize the yield of fermentable sugars on a per-hectare basis, to minimize the inputs of fertilizer, irrigation, fungicides and pesticides and to reduce the environmental footprint. Breeding strategies thus need to target biomass yield, biomass composition, maturity, pest and disease resistance and nutrient use efficiency. Furthermore, this chapter reviews the genetic basis of these traits and their potential application in breeding programs.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

High-throughput screening of environmental polysaccharide-degrading bacteria using biomass containment and complex insoluble substrates

Abstract Carbohydrate degradation by microbes plays an important role in global nutrient cycling, human nutrition, and biotechnological applications. Studies that focus on the degradation of complex recalcitrant polysaccharides are challenging because of the insolubility of these substrates as found in their natural contexts. Specifically, current methods to examine carbohydrate-based biomass degradation using bacterial strains or purified enzymes are not compatible with high-throughput screening using complex insoluble materials. In this report, we developed a small 3D printed filter device that fits inside a microplate well that allows for the free movement of bacterial cells, media, and enzymes while containing insoluble biomass. These devices do not interfere with standard microplate readers and can be used for both short- (24–48 h) and long-duration (> 100 h) experiments using complex insoluble substrates. These devices were used to quantitatively screen in a high-throughput manner environmental isolates for their ability to grow using lignocellulose or rice grains as a sole nutrient source. Additionally, we determined that the microplate-based containment devices are compatible with existing enzymatic assays to measure activity against insoluble biomass. Overall, these microplate containment devices provide a platform to study the degradation of complex insoluble materials in a high-throughput manner and have the potential to help uncover ecologically important aspects of bacterial metabolism as well as to accelerate biotechnological innovation.

3D printing↗
DOE OSTI2021

Unifying themes and distinct features of carbon and nitrogen assimilation by polysaccharide-degrading bacteria: a summary of four model systems

Our current understanding of enzymatic polysaccharide degradation has come from a huge number of in vitro studies with purified enzymes. While this vast body of work has been invaluable in identifying and characterizing novel mechanisms of action and engineering desirable traits into these enzymes, a comprehensive picture of how these enzymes work as part of a native in vivo system is less clear. Recently, several model bacteria have emerged with genetic systems that allow for a more nuanced study of carbohydrate active enzymes (CAZymes) and how their activity affects bacterial carbon metabolism. With these bacterial model systems it is now possible to not only study a single nutrient system in isolation (i.e. carbohydrate degradation and carbon metabolism), but also how multiple systems are integrated. Given that most environmental polysaccharides are carbon rich but nitrogen poor (e.g. lignocellulose), the interplay between carbon and nitrogen metabolism in polysaccharide-degrading bacteria can now be studied in a physiologically relevant manner. Therefore, in this review we have summarized what has been experimentally determined for CAZyme regulation, production, and export in relation to nitrogen metabolism for two Gram-positive (Caldicellulosiruptor bescii and Clostridium thermocellum) and two Gram-negative (Bacteroides thetaiotaomicron and Cellvibrio japonicus) polysaccharide-degrading bacteria. By comparing and contrasting these four bacteria we have highlighted the shared and unique features of each, with a focus on in vivo studies, in regard to carbon and nitrogen assimilation. Finally, we conclude with what we believe are two important questions that can act as guideposts for future work to better understand the integration of carbon and nitrogen metabolism in polysaccharide-degrading bacteria.

Cellvibrio japonicus↗
DOE OSTI2021

Major involvement of two laccase genes in conidial pigment biosynthesis in Aspergillus oryzae

Wild-type strains of Aspergillus oryzae develop yellow, yellow-green, green, or brown conidia. Previous reports suggested that the conidiation initiates with the biosynthesis of a yellow pigment YWA1 from acetyl-CoA by a polyketide synthase encoded by wA (AO090102000545). This is followed by the conversion to other pigment by a laccase encoded by yA (AO090011000755). Based on orthologous pathways in other aspergilli, it is reasonable to hypothesize that in addition to yA, AO090102000546 encoding laccase and AO090005000332 encoding Ayg1-like hydrolase play a role in A. oryzae conidial pigment biosynthesis. However, the involvement of these two genes in conidial pigmentation remains unclear. In this study, we tested this hypothesis by assessing the conidial colors of both disruption and overexpression mutants to verify whether AO090102000546 and AO090005000332 were associated with the conidial pigmentation. Here, observation of single, double, and triple disruptants of these three genes suggested that conidial pigments were synthesized by two laccase genes, AO090011000755 and AO090102000546, whereas Ayg1-like hydrolase gene AO090005000332 was proven to have no obvious association with the synthesis. This was corroborated by observing the phenotype of each overexpression mutant. Interestingly, AO090005000332 overexpression mutant produced smoky yellow-green conidia, different from the wild-type strain. Thus, the AO090005000332-encoded protein is likely to maintain the enzymatic activity. However, the expression level was observed to be one-third of that of AO090102000546 and one-seventh of that of AO090011000755. Consequently, apparent lack of obvious contribution of AO090005000332 to conidial pigmentation could be attributed to its low expression level. Expression analysis indicated similar profiles in several wild-type strains.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Thermophilic biocatalysts for one-step conversion of citrus waste into lactic acid

Agri-food residues offer significant potential as a raw material for the production of L-lactic acid through microbial fermentation. Weizmannia coagulans, previously known as Bacillus coagulans, is a spore-forming, lactic acid-producing, gram-positive, with known probiotic and prebiotic properties. This study aimed to evaluate the feasibility of utilizing untreated citrus waste as a sustainable feedstock for the production of L-lactic acid in a one-step process, by using the strain W. coagulans MA-13. By employing a thermophilic enzymatic cocktail (Cellic CTec2) in conjunction with the hydrolytic capabilities of MA-13, biomass degradation was enhanced by up to 62%. Moreover, batch and fed-batch fermentation experiments demonstrated the complete fermentation of glucose into L-lactic acid, achieving a concentration of up to 44.8 g/L. These results point to MA-13 as a microbial cell factory for one-step production of L-lactic acid, by combining cost-effective saccharification with MA-13 fermentative performance, on agri-food wastes. Moreover, the potential of this approach for sustainable valorization of agricultural waste streams is successfully proven.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Direct determination of cellulosic glucan content in starch-containing samples

A simple and highly selective analytical procedure is presented for the determination of cellulosic glucan content in samples that contain both cellulose and starch. This method eliminates the unacceptably large compounding errors of current two-measurement methods. If both starch and cellulose are present before analytical hydrolysis, both will be hydrolyzed to glucose causing bias and inaccuracy in the method. To prevent this interference, the removal of starch prior to cellulosic quantification is crucial. The method presented here is a concise in-series procedure with minimal measurements, eliminating large compounding errors. Sample preparation consists of a starch extraction employing enzymatic hydrolysis followed by a simple filtration and wash. The samples are then subjected to a two-stage acid hydrolysis. The concentration of glucose is determined by ion exchange high-performance liquid chromatography with a Pb 2+ column and a refractive index detector. The cellulosic glucan content is calculated based on the initial dry weight of the starting material. Data for the native biomass materials studied show excellent reproducibility, with coefficients of variance of 3.0% or less associated with the method. This selectivity for cellulosic glucan by the procedure was validated with several analytical techniques such as liquid chromatography coupled with mass spectrometry (LC–MS), Raman spectroscopy, and nuclear magnetic resonance.

09 BIOMASS FUELS↗
DOE OSTI2022

Pretreatment of lignocellulosic feedstocks for cellulose nanofibril production

Cellulose nanofibrils (CNFs) have attracted a great deal of research interest in recent years attributable to the low cost and abundance of lignocellulosic biomass from which they can be extracted. These materials have potential applications in a wide array of areas because of their unique properties such as ultra-high aspect ratios and specific strengths. However, the high energy required to extract CNFs from biomass through fibrillation often makes them prohibitively expensive or negates their inherent sustainability. As such, a variety of biomass treatments prior to fibrillation have been investigated by researchers to reduce the energy requirements of CNF extraction, improve the efficacy of biomass fibrillation and subsequent processes, and/or impart functionality in resulting nanofibrils. In this work, both widely used and emerging mechanical, chemical, and enzymatic pretreatments used prior to fibrillation of lignocellulosic biomass for CNF extraction are reviewed. Attention is given to the effect of these various pretreatments on the properties of the resulting CNFs. Finally, the energy consumption in fibrillation processes with and without the use of pretreatments is compared, and future perspectives on challenges and opportunities in lignocellulosic feedstock pretreatments are discussed.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Integrating the Fields of Catalysis: Active Site Engineering in Metal Cluster, Metal Organic Framework and Metal Single Site

Research evolved using nanoparticles synthesized and characterized under reaction conditions opened the door to study all three fields of catalysis: heterogeneous, homogenous, and enzyme. Fundamental studies of catalytic reactions ranging from hydrogenation to understand Fischer-Tropsch synthesis and isomerization ultimately led to the integration of three fields of catalysis. Our recent work on bridging heterogeneous, homogenous, and enzymatic catalysis was present including functionalization of dendrimer encapsulated metal clusters surface for lactonization, active site engineering in metal organic framework catalysts for methanol production and oligomerization, and single site catalyst for hydrogen production. We envision that the combination of active site engineering and unifying fields of catalysis could be applied to solve practical issues of science-based technology and develop new fields useful in energy research.

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

Deacetylation and Mechanical Refining Pathway for the Bioconversion of Sugarcane Bagasse

Advancing lignocellulose biorefining is imperative for the deployment of cellulosic (2G) biofuels. This work investigates the tailoring of the alkaline deacetylation and mechanical refining (DMR) pathway for the bioconversion of sugarcane bagasse. Experiments are conducted at laboratory and pilot scales, varying the pretreatment conditions (70–92 °C; 48–100 g NaOH /kg) and the mechanical refining technologies (PFI and disk refining). The pretreatments selectively solubilize acetyl groups (> 86%) and lignin (10–63%) while mostly preserving structural carbohydrates in the solid phase. Enzymatic hydrolysis generates hydrolysates of clean sugars (glucose and xylose), with sugar yields increasing up to 81% for glucose and 89% for xylose in response to delignification and mechanical refining. Biochemical methane potential assays reveal specific methane productions of up to 568 NmL CH₄ gVS⁻¹ for alkaline liquor monodigestion and 344 NmL CH₄ gVS⁻¹ for co-digestion with sugarcane vinasse from the conventional (1G) sugarcane ethanol, indicating a strong potential for bioenergy recovery from this process stream. Synergies are identified in integrating 1G ethanol, 2G DMR processing of bagasse, and anaerobic co-digestion of 1G vinasse and 2G DMR alkaline liquor. This technology enables sugarcane biorefineries to enhance the co-production of ethanol, methane, and concentrated streams of CO 2 .

09 BIOMASS FUELS↗
DOE OSTI2020

Enzyme interactions on lignocellulosic biomass structure

This chapter shows that, although well studied over the years, the cellulose enzymatic hydrolysis process has still many obstacles to be overcome or minimized. High enzyme loading and relatively long incubation periods are generally required for effective cellulose saccharification to be achieved. These limitations make the process unattractive from an economic perspective. Most studies show that the conversion rate of cellulose hydrolysis decreases over reaction time due to several factors that may inhibit, deactivate, or slow the work of enzymes. Some of these factors are inhibition by the product generated; inhibition/deactivation of enzymes by by-products generated during pretreatment (PT); limitation of mass transfer; shear stress by high stirring; air–liquid interfacial area; and unproductive adsorption on lignin or other compounds present in the biomass. The interaction between cellulases and the lignin present in these biomasses has a major negative impact on the process, with the source of the raw material and the type of PT used having a strong influence on it. Finally, the use of nonenzymatic proteins seems to be the best way to mitigate this problem.

20 FOSSIL-FUELED POWER PLANTS↗
DOE OSTI2021

Production of Biofuels from Biomass by Fungi

The use of abundantly available lignocellulosic biomass as a feedstock for biofuels has emerged as a sustainable alternative to fossil fuels. Industries across the world have shifted their focus to enhancing bioconversion through fungi, efficient and tractable organisms capable of producing valuable cost-effective enzymes. The many capabilities of fungal species offer opportunities for the tailored production of valuable compounds from a variety of substrates. This review details a high level examination of how fungal enzymes degrade plant polysaccharides to simple sugars through the sensitive coordination of transcription factors. Scientists have used a variety of tools like genetically engineering fungi, combining various species, and altering industrial/process conditions to enhance biomass deconstruction and fermentation while solving obstacles like inhibitory compounds. While ethanol and biodiesel are highlighted, additional biofuels are mentioned. These advances have uncovered themes like synergism and biocatalysis, led to the discovery of new fungal species, and revealed unique enzymatic mechanisms. Notably, this research highlights the complexity of metabolic systems within and between fungi. Fungi have been indispensable to the biofuel industry and future research will be crucial for energy sustainability.

Ottum, Eva MN↗
DOE OSTI2020

Pyridoxal 5'-phosphate dependent reactions: Analyzing the mechanism of aspartate aminotransferase

Enzyme catalysis is the primary activity in energy and information metabolism and enzyme cofactors are key to the catalytic ability of most enzymes. Pyridoxal 5'-phosphate (PLP) cofactor, derived from Vitamin B6, is widely distributed in nature and has significant latitude in catalytic diversity. X-ray crystallography has revealed the structures of diverse PLP dependent enzymes from multiple families. But these structures are incomplete, lacking the positions of protons essential for understanding enzymatic mechanisms. Here, we review the diversity of PLP and discuss the use of neutron crystallography and joint X-ray/neutron refinement of Fold Type I aspartate aminotransferase to visualize the positions of protons in both the internal and external aldimine forms. Strategies used to prepare extremely large crystals required for neutron diffraction and the approach to data refinement including the PLP cofactor are discussed. The observed positions of protons, including one located in a previously unknown low-barrier hydrogen bond, have been used to create more accurate models for computational analysis. The results revealed a new mechanism for the transaminase reaction where hyperconjugation is key to reducing the energy barrier which finally provides a clear explanation of the Dunathan alignment.

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

Biodiesel production from engineered sugarcane lipids under uncertain feedstock compositions: Process design and techno-economic analysis

In this study, different process schemes were designed and evaluated for biodiesel production from engineered cane lipids with uncertain fatty acid compositions. Four different process schemes were compared under (i) thermal glycerolysis and (ii) enzymatic glycerolysis approaches. These schemes were based on the biodiesel yield and economic indicators such as the net present value (NPV) and the minimum selling price (MSP) of biodiesel. A scheme with polar lipid separation under thermal glycerolysis resulted in the maximum NPV ($\$96.5$ million) and minimum MSP ($\$1107$ /ton biodiesel), respectively. Through local sensitivity analysis, it was concluded that the cane lipid percentage is the most significant factor influencing process economics. A conjoint analysis of the lipid procurement price and cane lipid percent suggested that 15% cane lipids with a low lipid procurement price ($\$0.536$ /kg) results in a positive NPV. When the cane lipid price is higher (> $\$0.80$ /kg), a 20% lipid content should be considered to achieve a positive NPV. At 20% cane lipids, the worst-case and best-case scenarios were evaluated by analyzing the interplay of the three most important parameters, Here, the best-case scenario revealed that the minimum NPV under any process scheme could yield more than $\$100$ million (or MSP: $\$0.80$ /L), and the worst-case analysis showed that losses incurred by the plant could be as high as 80 million (MSP: $\$1.36$ /L). A Monte Carlo simulation indicated that there is a 70% chance of the plant being profitable (NPV > 0).

09 BIOMASS FUELS↗
DOE OSTI2025

N-terminal domain swapping: A new paradigm for spermidine/spermine N -acetyltransferase (SSAT) protein structures?

Enterococcus faecalis is a multi-drug-resistant human pathogen that is found in a variety of environments and is challenging to treat. Under stress conditions, some bacteria regulate intracellular polyamine concentrations via polyamine acetyltransferases to reduce their toxicity. The E. faecalis genome encodes two polyamine acetyltransferases: PmvE and BltD. Both of these proteins belong to the Gcn5-related N-acetyltransferase (GNAT) superfamily. It is unclear why there are two enzymes with similar substrate specificities in this organism. To better understand the structure/function relationship of the E. faecalis BltD enzyme, we determined its crystal structure and performed additional assays to explore its oligomeric state and enzymatic activity. The goal was to determine whether there were structural or catalytic differences between this enzyme and other polyamine acetyltransferases that could explain this redundancy and be exploited for future development of targeted inhibitors for this important human pathogen. We found the BltD enzyme was structurally unique due to its N-terminal domain swapped dimer. However, this enzyme adopts a catalytically active monomer rather than dimer in solution. This indicates the crystal structure we obtained may represent a state that forms at high protein and salt concentrations and at low pH used during crystallization. The BltD dimer found in the crystal may represent a unique view of how an inhibitory peptide or molecule could be designed to occupy its active site. Additionally, this structure shows the extensive flexibility of the N-terminal portion of the E. faecalis BltD enzyme.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Variations in cell wall traits impact saccharification potential of Salix famelica and Salix eriocephala

Increasing global populations, finite arable land, and the anthropogenic release of carbon dioxide into the atmosphere are driving the search for bio-based alternatives to the petroleum-derived fuels and chemicals that underpin the global economy. With rapid growth rates, a propensity for coppicing, and a wide geographic range across Canada, native shrub willows (Salix spp.) are an attractive source of low-input, high-volume biomass. To date, most willow research has focused on increasing yields and improving cropping systems, while comparatively little work has been done to assess the intrinsic diversity in cell wall traits and bioenergy potential. In this study, we characterized the cell wall composition and wood ultrastructure of 338 xylem samples from two Canadian willow species, Salix famelica and Salix eriocephala, harvested from a common garden experimental plot. Lignin content ranged from 17.5–25.1% in S. famelica and 18.6–24.3% in S. eriocephala. Following alkali pretreatment with 62.5 mM NaOH at 90 °C for 3 h and a 70-h enzymatic digestion with Accellerase 1000, glucose release ranged from 23.0–38.9 wt% in S. famelica and from 20.5–37.7 wt% in S. eriocephala, while xylose release ranged from 9.4–14.9% in S. famelica and from 9.5–15.2% in S. eriocephala. Here, partial least squares regression modelling showed that lignin content and composition were important negative regulators of glucose release. Overall, this work highlights the innate variability in cell wall traits of native willows and identifies potential genotypes that should be considered in future breeding and deployment strategies for Canadian bioenergy production.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

New strategy for liquefying corn stover pellets

The movement of solid material into and between unit operations within a biorefinery is a bottleneck in reaching design capacity, with formation of biomass slurries needed to introduce feedstock. Corn stover slurries have been achieved from dilute acid, pretreated materials resulting in slurry concentrations of up to about 150 g/L, above which flowability is compromised. We report a new strategy to liquefy corn stover at higher solids concentration (300 g/L) by initially cooking it with the enzyme mimetic maleic acid at 40 mM and 150°C. This is followed by 6 h of enzymatic modification at 1 FPU (2.2 mg protein)/g solids, resulting in a yield stress of 171 Pa after 6 h and 58 Pa in 48 h compared to 6806 Pa for untreated stover. Mimetic treatment of corn stover pellets minimizes the inhibitory effect of xylo-oligomers on hydrolytic enzymes. Furthermore, this strategy allows for the delivery of solid lignocellulosic slurry into a pretreatment reactor by pumping, improving operability of a biorefinery.

09 BIOMASS FUELS↗