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At least 55 records · Page 3

Engineered Pseudomonas putida simultaneously catabolizes five major components of corn stover lignocellulose: Glucose, xylose, arabinose, p-coumaric acid, and acetic acid

Valorization of all major lignocellulose components, including lignin, cellulose, and hemicellulose is critical for an economically viable bioeconomy. In most biochemical conversion approaches, the standard process separately upgrades sugar hydrolysates and lignin. Here, we present a new process concept based on an engineered microbe that could enable simultaneous upgrading of all lignocellulose streams, which has the ultimate potential to reduce capital cost and enable new metabolic engineering strategies. Specifically, we engineered Pseudomonas putida, a robust microorganism capable of catabolizing aromatic compounds, organic acids, and D-glucose, to utilize D-xylose and L-arabinose by tuning D-xylose transport and pentose phosphate pathway flux. Distinct L-arabinose pathways enabled D-glucose, D-xylose, and L-arabinose co-utilization in minimal medium using model compounds as well as corn stover hydrolysate. After modifying catabolite repression, our engineered P. putida simultaneously co-utilized five representative compounds from cellulose, hemicellulose, and lignin, demonstrating the feasibility of simultaneously upgrading total lignocellulosic biomass to value-added chemicals.

Elmore, Joshua R.↗

In-depth understanding of molecular mechanisms of aldehyde toxicity to engineer robust Saccharomyces cerevisiae

Aldehydes are ubiquitous electrophilic compounds that ferment microorganisms including Saccharomyces cerevisiae encounter during the fermentation processes to produce food, fuels, chemicals, and pharmaceuticals. Aldehydes pose severe toxicity to the growth and metabolism of the S. cerevisiae through a variety of toxic molecular mechanisms, predominantly via damaging macromolecules and hampering the production of targeted compounds. Compounds with aldehyde functional groups are far more toxic to S. cerevisiae than all other functional classes, and toxic potency depends on physicochemical characteristics of aldehydes. The yeast synthetic biology community established a design–build–test–learn framework to develop S. cerevisiae cell factories to valorize the sustainable and renewable biomass, including the lignin-derived substrates. However, thermochemically pretreated biomass-derived substrate streams contain diverse aldehydes (e.g., glycolaldehyde and furfural), and biological conversions routes of lignocellulosic compounds consist of toxic aldehyde intermediates (e.g., formaldehyde and methylglyoxal), and some of the high-value targeted products have aldehyde functional group (e.g., vanillin and benzaldehyde). Numerous studies comprehensively characterized both single and additive effects of aldehyde toxicity via systems biology investigations, and novel molecular approaches have been discovered to overcome the aldehyde toxicity. Based on those novel approaches, researchers successfully developed synthetic yeast cell factories to convert lignocellulosic substrates to valuable products, including aldehyde compounds. Here, we highlight the salient relationship of physicochemical charac- teristics and molecular toxicity of aldehydes, the molecular detoxification and macromolecules protection mechanisms of aldehydes, and the advances of engineering robust S. cerevisiae against complex mixtures of aldehyde inhibitors.

59 BASIC BIOLOGICAL SCIENCES↗

A yeast platform for high-level synthesis of tetrahydroisoquinoline alkaloids

The tetrahydroisoquinoline (THIQ) moiety is a privileged substructure of many bioactive natural products and semi-synthetic analogs. Plants manufacture more than 3,000 THIQ alkaloids, including the opioids morphine and codeine. While microbial species have been engineered to synthesize a few compounds from the benzylisoquinoline alkaloid (BIA) family of THIQs, low product titers impede industrial viability and limit access to the full chemical space. Here we report a yeast THIQ platform by increasing production of the central BIA intermediate ( S )-reticuline to 4.6 g L –1 , a 57,000-fold improvement over our first-generation strain. We show that gains in BIA output coincide with the formation of several substituted THIQs derived from amino acid catabolism. We use these insights to repurpose the Ehrlich pathway and synthesize an array of THIQ structures. This work provides a blueprint for building diverse alkaloid scaffolds and enables the targeted overproduction of thousands of THIQ products, including natural and semi-synthetic opioids.

59 BASIC BIOLOGICAL SCIENCES↗

Characterizing and Engineering Trehalose Biosynthesis Pathways to Improve Acetate Tolerance in Pseudomonas putida KT2440

Alkaline pretreatment can depolymerize lignin into a diverse mixture of monomers and smaller compounds, enabling bioconversion of these compounds to value-added chemicals in engineered bacterial hosts such as Pseudomonas putida KT2440. Acetate and salts comprise approximately 8% and 32% of the lignin stream, respectively. High concentrations of these components can cause cell death in P. putida, so lignin-derived streams must be fed in lower amounts to decrease stress. Investigation of the mechanisms of bacterial tolerance to chemicals in lignin-rich substrates is therefore required to overcome this obstacle in lignin bioconversion. Previous work has shown that trehalose, an endogenously produced disaccharide, is involved in tolerance to heat, cold, and osmotic stress, as well as implicated in acid stress in other bacteria. As such, trehalose biosynthesis presents a useful target to increase acetate and osmotic tolerance in P. putida. This work investigates the native TreSA, TreSB, and TreY/TreZ trehalose biosynthesis pathways in this bacterial strain as well as the OtsAB pathway of Sphingobium sp. SYK-6. Overexpression of the OtsAB pathway in P. putida increased tolerance to acetate relative to wild-type. Additionally, functional knockouts of treSA, treSB, treY, and treZ in P. putida showed that interruption of any trehalose biosynthesis pathway, and, in the case of TreY/TreZ, interruption of the pathway at any point, significantly hindered growth in acetate as well as on glucose and LB broth. Each trehalose biosynthesis pathway was then engineered for overexpression in P. putida to determine whether overexpression of these genes conferred additional tolerance to acetate. The TreSA, TreSB, OtsA, and OtsB enzymes were also expressed and purified to determine the reaction rates and kinetics of these pathways. The hypothetical glycoside hydrolase family 15 protein, encoded in the gene located in between otsB and otsA in the Sphingobium operon, was purified as well to investigate its potential involvement in the OtsAB pathway. The findings of this work illuminated the mechanisms of trehalose biosynthesis in P. putida and identified genetic targets to improve strain tolerance to common components of alkaline-pretreated lignin streams. These findings could ultimately improve yields of desired products from lignin in engineered strains of P. putida.

alkaline pretreatment↗

Genetic tools for engineering Zymomonas mobilis , Cereibacter sphaeroides and Novosphingobium aromaticivorans to improve production of bioenergy compounds

Limited genetic tools for non-model bacteria are one of the limiting factors for genetic studies. This review compiles genetic tools used for three non-model alpha-proteobacteria, such as Zymomonas mobilis, Cereibacter (Rhodobacter) sphaeroides, and Novosphingobium aromaticivorans, which hold significant potential to produce industrially essential bioenergy compounds due to their distinctive metabolic pathways and resilience in extreme environments. Each of these strains has a unique genetic profile that enables them to efficiently carry out key reactions relevant to producing bioenergy compounds, such as converting sugars into bioenergy compounds and breaking down lignotoxins. Genetic tools can further optimize these strains for enhanced bioenergy compound production. This review explores the metabolic advantages of these organisms. It highlights the available array of genetic toolkits that can be shared among them to unlock their full potential for sustainable biofuel production.

Biofuel↗

Establishing a versatile toolkit of flux enhanced strains and cell extracts for pathway prototyping

Building and optimizing biosynthetic pathways in engineered cells holds promise to address societal needs in energy, materials, and medicine, but it is often time-consuming. Cell-free synthetic biology has emerged as a powerful tool to accelerate design-build-test-learn cycles for pathway engineering with increased tolerance to toxic compounds. However, most cell-free pathway prototyping to date has been performed in extracts from wildtype cells which often do not have sufficient flux towards the pathways of interest, which can be enhanced by engineering. Here, in this study, to address this gap, we create a set of engineered Escherichia coli and Saccharomyces cerevisiae strains rewired via CRISPR-dCas9 to achieve high-flux toward key metabolic precursors; namely, acetyl-CoA, shikimate, triose-phosphate, oxaloacetate, α-ketoglutarate, and glucose-6-phosphate. Cell-free extracts generated from these strains are used for targeted enzyme screening in vitro. As model systems, we assess in vivo and in vitro production of triacetic acid lactone from acetyl-CoA and muconic acid from the shikimate pathway. The need for these platforms is exemplified by the fact that muconic acid cannot be detected in wildtype extracts provided with the same biosynthetic enzymes. We also perform metabolomic comparison to understand biochemical differences between the cellular and cell-free muconic acid synthesis systems (E. coli and S. cerevisiae cells and cell extracts with and without metabolic rewiring). While any given pathway has different interfaces with metabolism, we anticipate that this set of pre-optimized, flux enhanced cell extracts will enable prototyping efforts for new biosynthetic pathways and the discovery of biochemical functions of enzymes.

59 BASIC BIOLOGICAL SCIENCES↗

Alkyl dialkoxyalkanoates as bioderived, high cetane diesel fuels

A fuel for an internal combustion engine includes a C 5 to C 30 dialkoxyalkanoate corresponding to formula (I), wherein the R 1 group is —H or a —CH 3 group, the R 2 and R 2 ′ groups are alkyl groups independently selected to have 1 to 9 carbon atoms; and the R 3 group is selected to have 1 to 9 carbon atoms. The compounds described herein may be used as neat fuels or mixed fuels (with diesel, biodiesel, jet fuel, marine fuel or other fuel compounds) in autoignition or spark ignition engines, such as diesel engines, gasoline (spark ignition) engines, MCCI, Homogeneous Charge Compression Ignition (HCCI) engines, or more generally in Low-Temperature Gasoline Combustion (LTGC) engines (using gasoline-like fuels), that have the high-efficiency advantages of HCCI but can operate with some level of charge inhomogeneities. Methods of making these compounds are environmentally friendly and can be done in a continuous manner.

Myllenbeck, Nicholas↗

Reference Correlations for the Density and Viscosity of Molten Alkali and Alkaline Earth Fluoride Salts

While there is a significant body of literature pertaining to thermophysical property measurements of molten salts, there is often a wide degree of variability among independent measurements of the same compounds. As such, the scientific community benefits greatly from an unbiased, independent assessment of duplicate datasets, so that reference correlations which describe these thermophysical properties as functions of temperature can be determined and then commonly used by researchers, scientists, and engineers. With regard to molten fluoride compounds, a significant time has elapsed since density and viscosity reference correlations have been determined; Janz conducted the most recent effort, in 1988, to provide reference correlations for the densities and viscosities of molten fluoride compounds via the National Standard Reference Data System coordinated by the National Bureau of Standards. Since then, new data have been published for molten fluoride compounds, and a new precedent has surfaced for putting forth reference correlations that involve fitting to multiple primary datasets. In this work, reference correlations are put forth for molten alkali and alkaline earth fluoride compounds in an effort to provide updated, improved correlations for general use. For molten alkali fluoride densities, estimated uncertainties with a 95% confidence interval are summarized as follows: LiF (0.63%), NaF (0.48%), KF (0.76%), RbF (0.93%), and CsF (0.75%). For molten alkaline earth fluoride densities, an estimated uncertainty was not able to be quantified for BeF 2 because of limited data; however, estimated uncertainties with a 95% confidence interval are summarized as follows for the remaining alkaline earth fluorides: MgF 2 (1.5%), CaF 2 (0.92%), SrF 2 (1.6%), and BaF 2 (0.23%). For molten alkali fluoride viscosities, uncertainty was not able to be quantified for RbF and CsF because of limited data; however, estimated uncertainties with a 95% confidence interval are summarized as follows for the remaining alkali fluorides: LiF (4.4%), NaF (3.0%), and KF (4.0%). For molten alkaline earth fluoride viscosities, limited consistent data resulted in the recommendation of single datasets (from literature) that are deemed to be the most trustworthy based on the quality of the underlying experimental studies.

Birri, A. [Oak Ridge National Laboratory (ORNL), O↗

Debottlenecking 4-hydroxybenzoate hydroxylation in Pseudomonas putida KT2440 improves muconate productivity from p -coumarate

The transformation of 4-hydroxybenzoate (4-HBA) to protocatechuate (PCA) is catalyzed by flavoprotein oxygenases known as para-hydroxybenzoate-3-hydroxylases (PHBHs). In Pseudomonas putida KT2440 (P. putida) strains engineered to convert lignin-related aromatic compounds to muconic acid (MA), PHBH activity is rate-limiting, as indicated by the accumulation of 4-HBA, which ultimately limits MA productivity. Here, we hypothesized that replacement of PobA, the native P. putida PHBH, with PraI, a PHBH from Paenibacillus sp. JJ-1b with a broader nicotinamide cofactor preference, could alleviate this bottleneck. Biochemical assays confirmed the strict preference of NADPH for PobA, while PraI can utilize either NADH or NADPH. Kinetic assays demonstrated that both PobA and PraI can utilize NADPH with comparable catalytic efficiency and that PraI also efficiently utilizes NADH at roughly half the catalytic efficiency. The X-ray crystal structure of PraI was solved and revealed absolute conservation of the active site architecture to other PHBH structures despite their differing cofactor preferences. To understand the effect in vivo, we compared three P. putida strains engineered to produce MA from p-coumarate (pCA), showing that expression of praI leads to lower 4-HBA accumulation and decreased NADP+/NADPH ratios relative to strains harboring pobA, indicative of a relieved 4-HBA bottleneck due to increased NADPH availability. In bioreactor cultivations, a strain exclusively expressing praI achieved a titer of 40 g/L MA at 100% molar yield and a productivity of 0.5 g/L/h. Altogether, this study demonstrates the benefit of sampling readily available natural enzyme diversity for debottlenecking metabolic flux in an engineered strain for microbial conversion of lignin-derived compounds to value-added products.

09 BIOMASS FUELS↗

Site Mixing for Engineering Magnetic Topological Insulators

The van der Waals compound, MnBi 2 Te 4 , is the first intrinsic magnetic topological insulator, providing a materials platform for exploring exotic quantum phenomena such as the axion insulator state and the quantum anomalous Hall effect. However, intrinsic structural imperfections lead to bulk conductivity, and the roles of magnetic defects are still unknown. With higher concentrations of the same types of magnetic defects, the isostructural compound MnSb 2 Te 4 is a better model system for a systematic investigation of the connections among magnetism, topology, and lattice defects. In this work, the impact of antisite defects on the magnetism and electronic structure is studied in MnSb 2 Te 4 . Mn-Sb site mixing leads to complex magnetic structures and tunes the interlayer magnetic coupling between antiferromagnetic and ferromagnetic. The detailed nonstoichiometry and site mixing of MnSb2Te4 crystals depend on the growth parameters, which can lead to ≈40% of Mn sites occupied by Sb and ≈15% of Sb sites by Mn in as-grown crystals. Single-crystal neutron diffraction and electron microscopy studies show nearly random distribution of the antisite defects. Band structure calculations suggest that the Mn-Sb site mixing favors a ferromagnetic interlayer coupling, consistent with experimental observation, but is detrimental to the band inversion required for a nontrivial topology. Overall, our results suggest a long-range magnetic order of Mn ions sitting on Bi sites in MnBi 2 Te 4 . The effects of site mixing should be considered in all layered heterostructures that consist of alternating magnetic and topological layers, including the entire family of MnTe(Bi 2 Te 3 )n, its Sb analogs, and their solid solution.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Air separation via a two-step solar thermochemical cycle based on (Ba,La) x Sr 1-x FeO 3-δ : Thermodynamic analysis

A two-step solar thermochemical cycle was considered for air separation to produce N2 based on (Ba,La) x Sr 1-x FeO 3-δ perovskite reduction/oxidation (redox) reactions for A-site fractions of 0 ≤ x ≤ 0.2. The cycle steps encompassed (1) thermal reduction and O 2 release via concentrated solar input and (2) re-oxidation with air to uptake O 2 and produce high-purity N 2 . Thermogravimetry at temperatures between 400 and 1100 °C in atmospheres of 0.005 to 90% O 2 /Ar at 1 bar was performed to measure equilibrium nonstoichiometries. The compound energy formalism was applied to model redox thermodynamics for both Ba 2+ and La 3+ substitution. Non-linear regression was used to determine the empirical parameters based on the thermogravimetric measurements. The model was used to define partial molar reaction enthalpies and entropies and predicted equilibrium oxygen nonstoichiometry as functions of oxide stoichiometry, site fraction, temperature, and O 2 partial pressure. The thermodynamic analysis showed the materials are appealing for air separation at temperatures below 800 °C.

42 ENGINEERING↗

High-precision vapor pressure measurement apparatus with facile and inexpensive construction

This study describes an apparatus for high-precision variable temperature measurement of liquid vapor pressure. The apparatus can be used to measure the vapor pressure using only 0.5 ml of the liquid sample. To evaluate the accuracy of the device measurement, water and 2-propanol are utilized as standard liquids, and their vapor pressure is measured with a maximum uncertainty of ~1%. This apparatus can be replicated using inexpensive and commonly used laboratory fittings and fixtures, making it an indispensable tool for synthetic chemists and chemical engineers involved in the iterative synthesis of compounds, targeting different vapor–liquid equilibrium regimes.

Engineering↗

Stress-tolerant non-conventional microbes enable next-generation chemical biosynthesis

Microbial chemical production is a rapidly growing industry, with much of the growth fueled by advances in synthetic biology. New approaches have enabled rapid strain engineering for the production of various compounds; however, translation to industry is often problematic because native phenotypes of model hosts prevent the design of new low-cost bioprocesses. Here, in this work, we argue for a new approach that leverages the native stress-tolerant phenotypes of non-conventional microbes that directly address design challenges from the outset. Growth at high temperature, high salt and solvent concentrations, and low pH can enable cost savings by reducing the energy required for product separation, bioreactor cooling, and maintaining sterile conditions. These phenotypes have the added benefit of allowing for the use of low-cost sugar and water resources. Non-conventional hosts are needed because these phenotypes are polygenic and thus far have proven difficult to recapitulate in the common hosts Escherichia coli and Saccharomyces cerevisiae.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Biological Lignin Valorization

Given lignin's heterogeneity, catalytic depolymerization results in aromatic compound mixtures, and conversion of this complex substrate to a single product is challenging. To that end, the Biological Lignin Valorization (BLV) project is pursuing biological funneling, wherein aromatic catabolic microbes are engineered to convert a mixture of lignin-derived compounds to a single product. Namely, we employ Pseudomonas putida and pursue atom-efficient products, such as muconic acid, which can be further converted to direct replacements or used in performance-advantaged bioproducts. Overall, biological lignin conversion can make major contributions to reduce the minimum fuel selling price of the integrated biorefinery. Early industrial efforts in this area are also leading to value-added products, including in collaboration with the BLV project. Primary challenges associated with BLV efforts include accessing bio-available monomers from lignin (with the Lignin Utilization project), enabling commercial titers, rates, and yields of bioproducts from lignin-derived compounds, and overcoming substrate and product toxicity. To date, we have 1) demonstrated 49 g/L of muconate from aromatic compounds and 4 g/L of muconate from lignin, 2) improved the toxicity tolerance of P. putida to key aromatic substrates, 3) debottlenecked biological funneling for higher rates, and 4) engineered P. putida to convert S, G, and H-type lignin-derived compounds to a single product.

BIOMASS FUELS,INORGANIC, ORGANIC, PHYSICAL, AND AN↗

From Salt to Electronics: Heteroepitaxy and GaAs Solar Cells

This paper presents work on the heteroepitaxy of salts, specifically fluorides, on semiconductor and heteroepitaxy of semiconductor on salts. Fluorides layers are deposited on commercial Gallium Arsenide (GaAs) wafers followed by the heteroepitaxial growth of GaAs using metal organic chemical vapor deposition (MOCVD). The fluoride layers consist of 2 lattice-engineered layers of alkaline-earth compounds to match with GaAs, and are used to sandwich another alkaline-earth compound with higher water-solubility as sacrificial layer. The triple fluoride layers enable liftoff of free-standing semiconductor films which can be further transferred to desirable substrates. 2D-X-ray Diffraction (2D-XRD) measurements confirm epitaxial growth of both the fluorides and the subsequently grown GaAs films. Single junction (SJ) solar cell devices based on thus prepared films show a power conversion efficiency (PCE) of 10.3% under 1 sun illumination. After the completion of device fabrications, the GaAs film is lifted off from the substrate by a novel water-assisted epitaxial liftoff (H 2 O-ELO) technique and transferred to a cheaper substrate. The original GaAs wafer is recycled and reused twice. Devices based on reused substrates show no significant degradation in performance. Lastly, the semiconductor-salt-semiconductor scheme has great implications in high performance, flexible, and large area electronics.

14 SOLAR ENERGY↗

Biological upgrading of pyrolysis-derived wastewater: Engineering Pseudomonas putida for alkylphenol, furfural, and acetone catabolism and (methyl)muconic acid production

While biomass-derived carbohydrates have been predominant substrates for biological production of renewable fuels, chemicals, and materials, organic waste streams are growing in prominence as potential alternative feedstocks to improve the sustainability of manufacturing processes. Catalytic fast pyrolysis (CFP) is a promising approach to generate biofuels from lignocellulosic biomass, but it generates a complex, carbon-rich, and toxic wastewater stream that is challenging to process catalytically but could be biologically upgraded to valuable co-products. Here, we implemented modular, heterologous catabolic pathways in the Pseudomonas putida KT2440-derived EM42 strain along with the overexpression of native toxicity tolerance machinery to enable utilization of 89% (w/w) of carbon in CFP wastewater. The dmp monooxygenase and meta-cleavage pathway from Pseudomonas putida CF600 were constitutively expressed to enable utilization of phenol, cresols, 2- and 3-ethyl phenol, and methyl catechols, and the native chaperones clpB, groES, and groEL were overexpressed to improve toxicity tolerance to diverse aromatic substrates. Next, heterologous furfural and acetone utilization pathways were incorporated, and a native alcohol dehydrogenase was overexpressed to improve methanol utilization, generating reducing equivalents. All pathways (encoded by genes totaling ~30 kilobases of DNA) were combined into a single strain that can catabolize a mock CFP wastewater stream as a sole carbon source. Further engineering enabled conversion of all aromatic compounds in the mock wastewater stream to (methyl)muconates with a ~90% (mol/mol) yield. Biological upgrading of CFP wastewater as outlined in this work provides a roadmap for future applications in valorizing other heterogeneous waste streams.

(methyl)muconates↗

Numerical Study of PAHs and Soot Emissions from Gasoline–Methanol, Gasoline–Ethanol, and Gasoline– n -Butanol Blend Surrogates

Soot formation is an intricate phenomenon, and soot propensity of a fuel is interwoven with the fuel composition, physical and chemical properties, and combustion environment. Here, the present study examines the hypothesis that in addition to the chemical composition of the fuel, the sooting nature of the fuel is closely coupled with its chemical property known as octane sensitivity (S). With this motivation, the present study numerically investigates the effects of gasoline surrogate composition and its property, octane sensitivity (S), on polycyclic aromatic hydrocarbons (PAHs) and soot emissions. Four-component toluene primary reference fuel (TPRF)–alcohol blends, comprising iso-octane, n-heptane, toluene, and one of the three different alcohols- methanol, ethanol, and n-butanol, are used as gasoline surrogates. A total of 320 TPRF–alcohol mixtures, with S in the range of 1–10, are examined under laminar counterflow diffusion flame conditions. A detailed chemical mechanism coupled with a comprehensive soot model, which includes reactions for soot inception, surface growth, PAH condensation, and oxidation, is adopted. The analysis indicates that the toluene content in the fuel mixture has a prominent effect, while the alcohol content and octane sensitivity of the fuel have a weak correlation with the PAHs and soot. Thus, it is not clear if any of these three variables, namely, toluene content in the fuel, alcohol content in the fuel, and S, are individually sufficient to characterize the PAHs and soot across various blends. For this reason, a new variable (X CHO ) based on the elemental composition of the fuel mixture is identified and it is shown that X CHO along with S of the fuel characterize soot emissions satisfactorily. Further, a reaction path analysis indicates that the efficacy of alcohols in reducing soot emissions follows the order: methanol > ethanol > n-butanol.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗