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At least 91 records · Page 5

Lignin to adipic acid in a high-yield chemical and biological redox process

Viable manufacturing pathways to produce bio-based chemicals from renewable feedstocks, such as lignin derived from plant biomass, are needed to decarbonize the chemicals manufacturing sector. Converting the recalcitrant lignin polymer to valuable bioproducts remains a longstanding challenge in biorefining, with the highest reported single-product yield from lignin currently around 20 wt%. Most existing lignin depolymerization strategies target aryl–ether bond cleavage, which can produce aromatic monomers in yields of only about 30 wt%, and still as complex mixtures with C–C-linked dimers and oligomers. The recalcitrance of these C–C linkages between aromatic moieties fundamentally limits single-product yields from lignin, prompting the development of strategies to efficiently cleave these C–C bonds. Here, in this study, we show how reductive processing of lignin from poplar accesses a hydrocarbon mixture of alkyl-aromatic monomers and oligomers that is privileged for oxidative conversion to monomeric aromatic carboxylic acids, comprising mostly benzoic acid and phthalic acid isomers in up to 73 wt% monomer yields, using a Co/Mn/Br catalyst. The soil bacterium Pseudomonas putida KT2440 was engineered to convert this mixture of aromatic carboxylic acids to muconolactone, a precursor to bio-based nylons, enabling final adipic acid yields up to 26 wt% (gram adipic acid per gram lignin) with a maximum theoretical yield of 57 wt%. This pairing of reductive and oxidative steps with lignin resembles processes in petrochemical refining and shows how lignin may be converted into a single, valuable bioproduct in high yields.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Engineering a universal and efficient platform for terpenoid synthesis in yeast

Engineering microbes for the production of valuable natural products is often hindered by the regulation of native competing metabolic networks in host. This is particularly evident in the case of terpenoid synthesis in yeast, where the canonical terpenoid precursors are tightly coupled to the biosynthesis of sterols essential for yeast viability. One way to circumvent this limitation is by engineering product pathways less connected to the host native metabolism. Here, we introduce a two-step isopentenol utilization pathway (IUP) in Saccharomyces cerevisiae to augment the native mevalonate pathway by providing a shortcut to the synthesis of the common terpenoid precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). As such, the IUP was capable of elevating the IPP/DMAPP pool by 147-fold compared with the native pathway. We further demonstrate that cofeeding isoprenol and prenol enhances geranyl diphosphate (GPP) content for monoterpene biosynthesis. More importantly, we established a synthetic three-step route for efficient synthesis of di-and tetraterpene precursor geranylgeranyl diphosphate (GGPP), circumventing the competition with farnesyl diphosphate (FPP) for sterol biosynthesis and elevating the GGPP level by 374-fold. We combine these IUP-supported precursor-forming platforms with downstream terpene synthases to harness their potential and improve the production of industrially relevant terpenoids by several fold. In conclusion, our exploration provides a universal and effective platform for supporting terpenoid synthesis in yeast.

59 BASIC BIOLOGICAL SCIENCES↗

Cloning and characterization of a panel of mitochondrial targeting sequences for compartmentalization engineering in Saccharomyces cerevisiae

Mitochondrion is generally considered as the most promising subcellular organelle for compartmentalization engineering. Much progress has been made in reconstituting whole metabolic pathways in the mitochondria of yeast to harness the precursor pools (i.e., pyruvate and acetyl-CoA), bypass competing pathways, and minimize transportation limitations. However, only a few mitochondrial targeting sequences (MTSs) have been characterized (i.e., MTS of COX4), limiting the application of compartmentalization engineering for multigene biosynthetic pathways in the mitochondria of yeast. In the present study, based on the mitochondrial proteome, a total of 20 MTSs were cloned and the efficiency of these MTSs in targeting heterologous proteins, including the Escherichia coli FabI and enhanced green fluorescence protein (EGFP) into the mitochondria was evaluated by growth complementation and confocal microscopy. After systematic characterization, six of the well!performed MTSs were chosen for the colocalization of complete biosynthetic pathways into the mitochondria. As proof of concept, the full alpha-santalene biosynthetic pathway consisting of 10 expression cassettes capable of converting acety coA to alpha-santalene was compartmentalized into the mitochondria, leading to a 3.7 fold improvement in the production of alpha-santalene. Furthermore, the newly characterized MTSs should contribute to the expanded metabolic engineering and synthetic biology toolbox for yeast mitochondrial compartmentalization engineering.

59 BASIC BIOLOGICAL SCIENCES↗

Data for Cloning and Characterization of a Panel of Mitochondrial Targeting Sequences for Compartmentalization Engineering in Saccharomyces cerevisiae

Mitochondrion is generally considered as the most promising subcellular organelle for compartmentalization engineering. Much progress has been made in reconstituting whole metabolic pathways in the mitochondria of yeast to harness the precursor pools (i.e., pyruvate and acetyl-CoA), bypass competing pathways, and minimize transportation limitations. However, only a few mitochondrial targeting sequences (MTSs) have been characterized (i.e., MTS of COX4), limiting the application of compartmentalization engineering for multigene biosynthetic pathways in the mitochondria of yeast. In the present study, based on the mitochondrial proteome, a total of 20 MTSs were cloned and the efficiency of these MTSs in targeting heterologous proteins, including the Escherichia coli FabI and enhanced green fluorescence protein (EGFP) into the mitochondria was evaluated by growth complementation and confocal microscopy. After systematic characterization, six of the well-performed MTSs were chosen for the colocalization of complete biosynthetic pathways into the mitochondria. As proof of concept, the full α-santalene biosynthetic pathway consisting of 10 expression cassettes capable of converting acetyl-coA to α-santalene was compartmentalized into the mitochondria, leading to a 3.7-fold improvement in the production of α-santalene. The newly characterized MTSs should contribute to the expanded metabolic engineering and synthetic biology toolbox for yeast mitochondrial compartmentalization engineering.

Conversion↗

A miniaturized feedstocks-to-fuels pipeline for screening the efficiency of deconstruction and microbial conversion of lignocellulosic biomass

Sustainably grown biomass is a promising alternative to produce fuels and chemicals and reduce the dependency on fossil energy sources. However, the efficient conversion of lignocellulosic biomass into biofuels and bioproducts often requires extensive testing of components and reaction conditions used in the pretreatment, saccharification, and bioconversion steps. This restriction can result in a significant and unwieldy number of combinations of biomass types, solvents, microbial strains, and operational parameters that need to be characterized, turning these efforts into a daunting and time-consuming task. Here we developed a high-throughput feedstocks-to-fuels screening platform to address these challenges. The result is a miniaturized semi-automated platform that leverages the capabilities of a solid handling robot, a liquid handling robot, analytical instruments, and a centralized data repository, adapted to operate as an ionic-liquid-based biomass conversion pipeline. The pipeline was tested by using sorghum as feedstock, the biocompatible ionic liquid cholinium phosphate as pretreatment solvent, a “one-pot” process configuration that does not require ionic liquid removal after pretreatment, and an engineered strain of the yeast Rhodosporidium toruloides that produces the jet-fuel precursor bisabolene as a conversion microbe. By the simultaneous processing of 48 samples, we show that this configuration and reaction conditions result in sugar yields (~70%) and bisabolene titers (~1500 mg/L) that are comparable to the efficiencies observed at larger scales but require only a fraction of the time. We expect that this Feedstocks-to-Fuels pipeline will become an effective tool to screen thousands of bioenergy crop and feedstock samples and assist process optimization efforts and the development of predictive deconstruction approaches.

09 BIOMASS FUELS↗

Current State, Challenges, and Opportunities in Genome-Scale Resource Allocation Models: A Mathematical Perspective

Stoichiometric genome-scale metabolic models (generally abbreviated GSM, GSMM, or GEM) have had many applications in exploring phenotypes and guiding metabolic engineering interventions. Nevertheless, these models and predictions thereof can become limited as they do not directly account for protein cost, enzyme kinetics, and cell surface or volume proteome limitations. Lack of such mechanistic detail could lead to overly optimistic predictions and engineered strains. Initial efforts to correct these deficiencies were by the application of precursor tools for GSMs, such as flux balance analysis with molecular crowding. In the past decade, several frameworks have been introduced to incorporate proteome-related limitations using a genome-scale stoichiometric model as the reconstruction basis, which herein are called resource allocation models (RAMs). This review provides a broad overview of representative or commonly used existing RAM frameworks. This review discusses increasingly complex models, beginning with stoichiometric models to precursor to RAM frameworks to existing RAM frameworks. RAM frameworks are broadly divided into two categories: coarse-grained and fine-grained, with different strengths and challenges. Discussion includes pinpointing their utility, data needs, highlighting framework strengths and limitations, and appropriateness to various research endeavors, largely through contrasting their mathematical frameworks. Finally, promising future applications of RAMs are discussed.

59 BASIC BIOLOGICAL SCIENCES↗

Evolutionary flexibility and rigidity in the bacterial methylerythritol phosphate (MEP) pathway

Terpenoids are a diverse class of compounds with wide-ranging uses including as industrial solvents, pharmaceuticals, and fragrances. Efforts to produce terpenoids sustainably by engineering microbes for fermentation are ongoing, but industrial production still largely relies on nonrenewable sources. The methylerythritol phosphate (MEP) pathway generates terpenoid precursor molecules and includes the enzyme Dxs and two iron–sulfur cluster enzymes: IspG and IspH. IspG and IspH are rate limiting-enzymes of the MEP pathway but are challenging for metabolic engineering because they require iron–sulfur cluster biogenesis and an ongoing supply of reducing equivalents to function. Therefore, identifying novel alternatives to IspG and IspH has been an on-going effort to aid in metabolic engineering of terpenoid biosynthesis. We report here an analysis of the evolutionary diversity of terpenoid biosynthesis strategies as a resource for exploration of alternative terpenoid biosynthesis pathways. Using comparative genomics, we surveyed a database of 4,400 diverse bacterial species and found that some may have evolved alternatives to the first enzyme in the pathway, Dxs making it evolutionarily flexible. In contrast, we found that IspG and IspH are evolutionarily rigid because we could not identify any species that appear to have enzymatic routes that circumvent these enzymes. The ever-growing repository of sequenced bacterial genomes has great potential to provide metabolic engineers with alternative metabolic pathway solutions. With the current state of knowledge, we found that enzymes IspG and IspH are evolutionarily indispensable which informs both metabolic engineering efforts and our understanding of the evolution of terpenoid biosynthesis pathways.

59 BASIC BIOLOGICAL SCIENCES↗

Organo-Nanocups Assist the Formation of Ultra-Small Palladium Nanoparticle Catalysts for Hydrogen Evolution Reaction

Ultra-small palladium nanoparticles were synthesized and applied as catalysts for a hydrogen evolution reaction. The palladium metal precursor was produced via beta-cyclodextrin as organo-nanocup (ONC) capping agent to produce ultra-small nanoparticles used in this study. The produced ~3 nm nanoparticle catalyst was then characterized via X-ray diffraction (XRD), transmission electron microscopy (TEM), ultraviolet-visible spectroscopy (UV-Vis), and Fourier transform infrared spectroscopy (FTIR) to confirm the successful synthesis of ~3 nm palladium nanoparticles. The nanoparticles’ catalytic ability was explored via the hydrolysis reaction of sodium borohydride. The palladium nanoparticle catalyst performed best at 303 K at a pH of 7 with 925 μmol of sodium borohydride having an H 2 generation rate of 1.431 mL min -1 mL cat -1 . The activation energy of the palladium catalyst was calculated to be 58.9 kJ/mol.

36 MATERIALS SCIENCE↗

Walking the ‘design–build–test–learn’ cycle: flux analysis and genetic engineering reveal the pliability of plant central metabolism

Oilseeds are of great economic importance for food and animal feed and their contribution to renewable energy production. Soybean seeds (Glycine max (L.) Merr.) contain c. 40% protein, 20% oil, and 30% carbohydrate (Song et al., 2023). Due to the massive scale of soybean production worldwide, even small improvements in seed protein and oil content make economic sense (Song et al., 2023). Successful manipulation of seed composition largely depends on a thorough understanding of the processes and pathways involved in the biosynthesis of fatty acids and amino acids, which are the building blocks of lipids and proteins. Rational engineering of the synthesis of storage reserves, that is, the rerouting of metabolic flux in central metabolism, is difficult to accomplish due to the complexity of the central metabolic network, the intricate regulation of its enzymes at multiple levels, and the often-unpredictable effects of genetic manipulation (Sweetlove et al., 2017). Therefore, the advancement of our understanding of central metabolism and its control of carbon partitioning requires following an iterative ‘design–build–test–learn’ (DBTL) cycle (Lin & Eudes, 2020) where metabolic flux analysis and hypothesis testing by transgenic approaches are important components. Previous metabolic studies on soybeans using isotopic tracers and metabolic flux analysis have provided insight into how lipid and protein biosynthesis occurs simultaneously during seed development (Allen et al., 2009; Allen & Young, 2013; Kambhampati et al., 2021). In an article published in this issue of New Phytologist, Morley et al. (2023; 1834–1851) put the insights they have gained into the delivery of metabolic precursors and energy cofactors to oil synthesis to the test and arrive at a successful metabolic engineering design. They show that an increase in seed oil content in soybeans can be achieved by overexpression of malic enzyme (ME) during seed development. Malic enzyme refers to a class of decarboxylating malate dehydrogenase enzymes that oxidize malate with NAD + or NADP + as redox cofactor while generating pyruvate and CO 2 . Like higher plants in general, soybean has distinct NADH- or NADPH-producing ME isoforms localized to the cytosol, plastid, or mitochondria (Gerrard Wheeler et al., 2016). As Morley et al. show, an increase in seed oil can be achieved in particular when a NADP+-dependent enzyme isoform (EC 1.1.1.40) is overexpressed in the plastid. Given the complex compartmentalization of pyruvate, malate, and redox metabolism (Fig. 1), increased oil production appears to depend on additional pyruvate and reducing equivalents being produced in the same compartment where de novo fatty acid biosynthesis occurs: the plastid.

59 BASIC BIOLOGICAL SCIENCES↗

Advances in Engineering Nucleotide Sugar Metabolism for Natural Product Glycosylation in Saccharomyces cerevisiae

Glycosylation is a ubiquitous modification present across all of biology, affecting many things such as physicochemical properties, cellular recognition, subcellular localization, and immunogenicity. Nucleotide sugars are important precursors needed to study glycosylation and produce glycosylated products. Saccharomyces cerevisiae is a potentially powerful platform for producing glycosylated biomolecules, but it lacks nucleotide sugar diversity. Nucleotide sugar metabolism is complex, and understanding how to engineer it will be necessary to both access and study heterologous glycosylations found across biology. This review overviews the potential challenges with engineering nucleotide sugar metabolism in yeast from the salvage pathways that convert free sugars to their associated UDP-sugars to de novo synthesis where nucleotide sugars are interconverted through a complex metabolic network with governing feedback mechanisms. Finally, recent examples of engineering complex glycosylation of small molecules in S. cerevisiae are explored and assessed.

59 BASIC BIOLOGICAL SCIENCES↗

LES and RANS Spray Combustion Analysis of OME 3-5 and n-Dodecane

Clean-burning oxygenated and synthetic fuels derived from renewable power, so-called e-fuels, are a promising pathway to decarbonize compression–ignition engines. Polyoxymethylene dimethyl ethers (PODEs or OMEs) are one candidate of such fuels with good prospects. Their lack of carbon-to-carbon bonds and high concentration of chemically bound oxygen effectively negate the emergence of polycyclic aromatic hydrocarbons (PAHs) and even their precursors like acetylene (C 2 H 2 ), enabling soot-free combustion without the soot-NO x trade-off common for diesel engines. The differences in the spray combustion process for OMEs and diesel-like reference fuels like n-dodecane and their potential implications on engine applications include discrepancies in the observed ignition delay, the stabilized flame lift-off location, and significant deviations in high-temperature flame morphology. For CFD simulations, the accurate modeling and prediction of these differences between OMEs and n-dodecane proved challenging. This study investigates the spray combustion process of an OME 3 − 5 mixture and n-dodecane with advanced optical diagnostics, Reynolds-Averaged Navier–Stokes (RANS), and Large-Eddy Simulations (LESs) within a constant-volume vessel. Cool-flame and high-temperature combustion were measured simultaneously via high-speed (50 kHz) imaging with formaldehyde (CH 2 O) planar laser-induced fluorescence (PLIF) representing the former and line-of-sight OH* chemiluminescence the latter. Both RANS and LES simulations accurately describe the cool-flame development process with the formation of CH 2 O. However, CH 2 O consumption and the onset of high-temperature reactions, signaled by the rise of OH* levels, show significant deviations between RANS, LES, and experiments as well as between n-dodecane and OME. A focus is set on the quality of the simulated results compared to the experimentally observed spatial distribution of OH*, especially in OME fuel-rich regions. The influence of the turbulence modeling is investigated for the two distinct ambient temperatures of 900 K and 1200 K within the Engine Combustion Network Spray A setup. The capabilities and limitations of the RANS simulations are demonstrated with the initial cool-flame propagation and periodic oscillations of CH 2 O formation/consumption during the quasi-steady combustion period captured by the LES.

CFD↗

Porous Polymer Structures with Tunable Mechanical Properties Using a Water Emulsion Ink

Recently, the manufacturing of porous polydimethylsiloxane (PDMS) with engineered porosity has gained considerable interest due to its tunable material properties and diverse applications. An innovative approach to control the porosity of PDMS is to use transient liquid phase water to improve its mechanical properties, which has been explored in this work. Adjusting the ratios of deionized water to the PDMS precursor during blending and subsequent curing processes allows for controlled porosity, yielding water emulsion foam with tailored properties. The PDMS-to-water weight ratios were engineered ranging from 100:0 to 10:90, with the 65:35 specimen exhibiting the best mechanical properties with a Young’s Modulus of 1.17 MPa, energy absorption of 0.33 MPa, and compressive strength of 3.50 MPa. This led to a porous sample exhibiting a 31.46% increase in the modulus of elasticity over a bulk PDMS sample. Dowsil SE 1700 was then added, improving the storage capabilities of the precursor. The optimal storage temperature was probed, with -60 °C resulting in great pore stability throughout a three-week duration. The possibility of using these water emulsion foams for paste extrusion additive manufacturing (AM) was also analyzed by implementing a rheological modifier, fumed silica. Fumed silica’s impact on viscosity was examined, revealing that 9 wt% of silica demonstrates optimal rheological behaviors for AM, bearing a viscosity of 10,290 Pa·s while demonstrating shear-thinning and thixotropic behavior. This study suggests that water can be used as pore-formers for PDMS in conjunction with AM to produce engineered materials and structures for aerospace, medical, and defense industries as sensors, microfluidic devices, and lightweight structures.

36 MATERIALS SCIENCE↗

Engineering an aldoxime dehydratase with high activity and isomer tolerance for biosynthesis of an O -protected primary cyanohydrin

O-protected primary cyanohydrins (glycolonitriles) are important building blocks for many difunctionalized compounds and precursors to known bioactive molecules. Their synthesis, however, utilizes toxic cyanide, which raises significant safety concerns for industrial synthesis. Here, in this study, we present a cyanide-free enzymatic synthesis of an o-benzyl protected primary cyanohydrin from an (E)- or (Z)-α-oxygen protected aldoxime using an engineered aldoxime dehydratase enzyme from Bacillus sp. OxB-1 (OxdB). In contrast to many evolved enzymes that tend to “specialize” as their activity increases, we used directed evolution to engineer OxdB for efficient dehydration of both isomers in a mixture of (E)- or (Z)-α-oxygen aldoximes with high activity and substrate loading to achieve near quantitative yield. Using this enzyme, we further demonstrate a cyanide-free chemoenzymatic pathway to an o-protected primary cyanohydrin starting from a readily available aldehyde, where the aldehyde is first condensed with hydroxylamine, followed by dehydration using our evolved enzyme. This pathway was readily scaled up to 1 g scale with high substrate loading, demonstrating its utility in industrial synthesis of these important building block functional groups.

Aldoxime dehydratase↗

Analysis of the cyanobacterial amino acid metabolism with a precise genome-scale metabolic reconstruction of Anabaena sp. UTEX 2576

Filamentous cyanobacteria such as Anabaena sp. UTEX 2576 (a.k.a., Nostoc sp. PCC 7120) are a sustainable platform for commodity and specialty chemical production. Anabaena is a model cyanobacterium adopted to study production of nitrogen-containing metabolites useful for chemical, cosmetic, and pharmaceutical industries. Therefore, a precise description of the Anabaena metabolic network is desired to analyze their amino-acid metabolism and elucidate potential applications of these cyanobacteria as host organisms for biotechnological production. Secondary metabolite production depends on the metabolic availability of amino acids. We provide new insight on the biotechnological utilization of Anabaena after predicting phycocyanobilin and amino-acid production rates, using a genome-scale metabolic model (iDN1004). This metabolic reconstruction is a highly comprehensive representation of the global metabolism of Anabaena, which also contains experimental biomass equations and constraints under photoautotrophic and photodiazotrophic growth. Modelling results ranked proteinogenic amino acids based on predicted metabolic fluxes through amino-acid producing reactions. From these, l-aspartate, glycine, l-serine, l-valine, l-alanine, l-threonine, and l-leucine were selected as the best branching points to conduct metabolic engineering, where l-aspartate, l-serine, l-valine and glycine serve as potential precursors of the secondary metabolites Schizokinen (a siderophore), Sphingosine (a ceramide), Lyngbyatoxin A (an alkaloid), and Shinorine (a sunscreen).

59 BASIC BIOLOGICAL SCIENCES↗

Molecular Additive Engineering for Process-Humidity Robustness and Reproducible Fabrication of Perovskite Solar Cells and Modules

The commercialization of perovskite solar cells (PSCs) faces significant challenges due to their sensitivity to environmental humidity, which compromises film crystallization and device stability. Here, we introduce diphenylvinylphosphine (DPVP) as a Lewis base additive that enhances the performance and reproducibility of PSCs fabricated under ambient-air conditions. DPVP suppresses moisture-induced defect formation and stabilizes crystallization within realistic process-humidity ranges (20–40% relative humidity) commonly encountered in laboratory and pilot-scale manufacturing environments. It improves film uniformity, reduces trap densities, and yields highly reproducible device performance, enabling champion PCEs of 24.2% in small-area devices and 20.5% in blade-coated 12 cm 2 mini-modules. Furthermore, DPVP-assisted modules exhibit enhanced stability, retaining over 85% of their initial efficiency after 900 h of maximum power point tracking (MPPT) at 65 °C. This study demonstrates a humidity-resilient and scalable additive strategy for ambient-air perovskite photovoltaic manufacturing.

defect passivation↗

Chemistry and Interfacial Structure Promoting Quasi-van der Waals Epitaxial Growth of WS 2 Nanosheets on Sapphire for Prospective Application in Field-Effect Transistors

How do chemical and structural modifications to the supporting crystal surface affect the subsequent van der Waals (vdW) or quasi(Q)-vdW epitaxial growth of 2D nanocrystals? Developing an atomic-scale picture of such an interfacial system is crucial for understanding its impact on the physical and chemical properties of the supported 2D materials. The elucidation of the interfacial structure and chemistry needed to promote the Q-vdW epitaxial growth of 2D tungsten disulfide (WS 2 ) nanocrystals contributes to the growth mechanism understanding, thus pushing forward the integration of such atomically thin semiconductors toward real field-effect transistor applications. In addition to an atomic-force microscopy top view, we showcase a combination of X-ray techniques for a top-to-bottom investigation of the complexities of the buried interface structures. Furthermore, this approach uses X-ray photoelectron spectroscopy, X-ray standing wave excited X-ray fluorescence, and crystal truncation rod scattering to produce a highly resolved chemical-state-specific 3D atomic map for the extended interface structure of WS 2 /α-Al 2 O 3 (001). Employing these detailed analysis methods, along with density functional theory to further refine the picoscale structure, we demonstrate how two different types of interface engineering during the pregrowth stage lead to significant differences in the chemical and structural modifications to the terminal surface of c-face sapphire, which in turn leads to substantial differences in the submonolayer growth of supported WS 2 2D nanocrystals in terms of lateral domain sizes, epitaxial registry, vdW gaps, and stability.

36 MATERIALS SCIENCE↗