Transcriptomic analysis of a Clostridium thermocellum strain engineered to utilize xylose: responses to xylose versus cellobiose feeding
Not Available
59 BASIC BIOLOGICAL SCIENCES↗
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Results for “Strain engineering”
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Strain engineering a persistent spin helix with infinite spin lifetime
Persistent spin textures (PSTs) in solid-state materials arise from a unidirectional spin-orbit field in momentum space and offer a route to deliver long carrier spin lifetimes sought for future quantum microelectronic devices. Nonetheless, few three-dimensional materials are known to host PSTs owing to crystal symmetry and chemical requirements. There are even fewer examples demonstrated experimentally. Here we report that high-quality persistent spin textures can be obtained in the polar point groups containing an odd number of mirror operations. We use representation theory analysis and electronic structure calculations to formulate general discovery principles to identify PSTs hidden in known complex ternary layered and perovskite structures with large electric polarizations. We then show some of these materials exhibit PSTs without requiring any special crystalline symmetries. This finding removes the limitation imposed by mirror-symmetry protected PSTs that has limited compound discovery. Our general design approach enables the pursuit of persistent spin helices in materials exhibiting the C 3 v crystal class adopted by many quantum materials exhibiting large Rashba coefficients.
36 MATERIALS SCIENCE↗
Strain engineering of diamond microstructures by trench filling and oxidation.
Abstract not provided.
Sapkota, Keshab↗
Engineering the electronic and strained interface for high activity of PdM core @Pt monolayer electrocatalysts for oxygen reduction reaction
Alloyed nanoparticles with core-shell structures provide a favorable model to modulate interfacial interaction and surface structures at the atomic level, which is important for designing electrocatalysts with high activity and durability. Herein, core-shell structured Pd 3 M@Pt/C nanoparticles with binary PdM alloy cores (M = Fe, Ni, and Co) and a monolayer Pt shell were successfully synthesized with diverse interfaces. Among these, Pd 3 Fe@Pt/C exhibited the best oxygen reduction reaction catalytic performance, roughly 5.4 times more than that of the commercial Pt/C catalyst used as reference. The significantly enhanced activity is attributed to the combined effects of strain engineering, interfacial electron transfer, and improved Pt utilization. Density functional theory simulations and extended X-ray absorption fine structure analysis revealed that engineering the alloy core with moderate lattice mismatch and alloy composition (Pd 3 Fe) optimizes the surface oxygen adsorption energy, thereby rendering excellent electrocatalytic activity. Finally, future researches may use this study as a guide on the construction of highly effective core-shell electrocatalysts for various energy conversions and other applications.
25 ENERGY STORAGE↗
Identification and characterization of proteins of unknown function (PUFs) in Clostridium thermocellum DSM 1313 strains as potential genetic engineering targets
Abstract Background Mass spectrometry-based proteomics can identify and quantify thousands of proteins from individual microbial species, but a significant percentage of these proteins are unannotated and hence classified as proteins of unknown function (PUFs). Due to the difficulty in extracting meaningful metabolic information, PUFs are often overlooked or discarded during data analysis, even though they might be critically important in functional activities, in particular for metabolic engineering research. Results We optimized and employed a pipeline integrating various “guilt-by-association” (GBA) metrics, including differential expression and co-expression analyses of high-throughput mass spectrometry proteome data and phylogenetic coevolution analysis, and sequence homology-based approaches to determine putative functions for PUFs in Clostridium thermocellum . Our various analyses provided putative functional information for over 95% of the PUFs detected by mass spectrometry in a wild-type and/or an engineered strain of C. thermocellum . In particular, we validated a predicted acyltransferase PUF (WP_003519433.1) with functional activity towards 2-phenylethyl alcohol, consistent with our GBA and sequence homology-based predictions. Conclusions This work demonstrates the value of leveraging sequence homology-based annotations with empirical evidence based on the concept of GBA to broadly predict putative functions for PUFs, opening avenues to further interrogation via targeted experiments.
09 BIOMASS FUELS↗
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↗
Orientation-Controlled Large-Area Epitaxial PbI 2 Thin Films with Tunable Optical Properties
Lead iodide (PbI 2 ) as a layered material has emerged as an excellent candidate for optoelectronics in the visible and ultraviolet regime. Micrometer-sized flakes synthesized by mechanical exfoliation from bulk crystals or by physical vapor deposition have shown a plethora of applications from low-threshold lasing at room temperature to high-performance photodetectors with large responsivity and faster response. However, large-area centimeter-sized growth of epitaxial thin films of PbI 2 with well-controlled orientation has been challenging. Additionally, the nature of grain boundaries in epitaxial thin films of PbI 2 remains elusive. Here, we use mica as a model substrate to unravel the growth mechanism of large-area epitaxial PbI 2 thin films. The partial growth leading to uncoalesced domains reveals the existence of inversion domain boundaries in epitaxial PbI 2 thin films on mica. Combining the experimental results with first-principles calculations, we also develop an understanding of the thermodynamic and kinetic factors that govern the growth mechanism, which paves the way for the synthesis of high-quality large-area PbI 2 on other substrates and heterostructures of PbI 2 on single-crystalline graphene. Here, the ability to reproducibly synthesize high-quality large-area thin films with precise control over orientation and tunable optical properties could open up unique and hitherto unavailable opportunities for the use of PbI 2 and its heterostructures in optoelectronics, twistronics, substrate engineering, and strain engineering.
2D materials↗
The strain-induced transitions of the piezoelectric, pyroelectric, and electrocaloric properties of the CuInP 2 S 6 films
Low-dimensional ferroelectrics, ferrielectrics, and antiferroelectrics are of urgent scientific interest due to their unusual polar, piezoelectric, electrocaloric, and pyroelectric properties. The strain engineering and strain control of the ferroelectric properties of layered two-dimensional van der Waals materials, such as CuInP 2 (S,Se) 6 monolayers, thin films, and nanoflakes, are of fundamental interest and especially promising for their advanced applications in nanoscale nonvolatile memories, energy conversion and storage, nano-coolers, and sensors. Here, we study the polar, piezoelectric, electrocaloric, and pyroelectric properties of thin strained films of a ferrielectric CuInP 2 S 6 covered by semiconducting electrodes and reveal an unusually strong effect of a mismatch strain on these properties. In particular, the sign of the mismatch strain and its magnitude determine the complicated behavior of piezoelectric, electrocaloric, and pyroelectric responses. The strain effect on these properties is opposite, i.e., “anomalous,” in comparison with many other ferroelectric films, for which the out-of-plane remanent polarization, piezoelectric, electrocaloric, and pyroelectric responses increase strongly for tensile strains and decrease or vanish for compressive strains.
antiferroelectricity↗
Effect of Mechanical Deformation on the Dielectric Electric Field in Dynamic Umbilical Cables
Wave energy converter (WEC) systems have unique umbilical cable design requirements compared to conventional marine designs. Due to their dynamic nature, WEC umbilical cables are required to handle increased loads and larger motions over longer deployment scenarios. However, the life expectancy of dynamic umbilical cables is predominantly analyzed for mechanical fatigue, with little consideration given to the effect of mechanical stress on the response of the dielectric as it has been previously assumed that the non-polymeric components will fail prior to the polymeric components. In this work, we explore the effects of mechanical bending on the concentration of the electric field in the insulation of a conceptual three-core dynamic umbilical cable to determine the limiting requirements for life expectancy. A conceptual industrial schematic of a medium voltage dynamic umbilical cable was used as the basis for the WEC system under study. Simulations on the dynamic umbilical cable were performed using COMSOL Multiphysics®. Mechanical loads up to the calculated limit (2.64 m minimum bend radius or 388 kN transverse load) were applied to the dynamic umbilical in a step-wise fashion with one end of the umbilical cable fixed. One-way coupling in three-dimensions was conducted by first determining the engineering strains, then using the engineering strains as the initial condition for determination of the Green-Lagrange strains, and lastly calculating the electric field in the deformed dielectric. Based upon the input load, deformation of the dielectric at the minimum bend radius produced an increase in the electric field of more than 12% when compared to the undeformed umbilical cable, which may lead to dielectric breakdown of the insulation prior to mechanical failure of the umbilical cable.
Spencer, Mychal P.↗
The role of AdhE mutations in Thermoanaerobacterium saccharolyticum
ABSTRACT Thermoanaerobacterium saccharolyticum is a thermophilic anaerobic bacterium that natively ferments a variety of hemicellulose substrates to organic acids and alcohols. It has recently been engineered to produce ethanol at high yield and titer; however, it uses a unique metabolic pathway for ethanol production that is poorly characterized. One of the distinctive aspects of this pathway is the presence of acetyl-CoA as an intermediate metabolite. In this organism, acetyl-CoA is converted to ethanol by a bifunctional AdhE enzyme. This enzyme has been a frequent target for mutations, and in many cases, the function of these mutations was unknown. Using a combination of genetic modifications, enzyme assays, and computational analysis, we have developed a better understanding of how mutations in AdhE affect ethanol production in the engineered homoethanologen strain. We identify a set of approximately interchangeable AdhE mutations (G544D, T597K, T597I, and T605I), whose function is to disrupt the activity of the alcohol dehydrogenase (ADH) domain of AdhE. This reduces NADH-linked ADH activity, which dramatically increases ethanol tolerance and changes the overall stoichiometry of acetaldehyde to ethanol conversion. Furthermore, our improved understanding of the function of these AdhE mutations calls into question a proposed feature of AdhE enzymes known as substrate channeling—direct transfer of acetaldehyde between the two domains of the AdhE enzyme. This improved the understanding of the role of AdhE mutations in T. saccharolyticum and provides deeper insights into the function of the unique ethanol production pathway in this organism. IMPORTANCE Many anaerobic bacteria maintain redox equilibrium by producing reduced organic compounds such as ethanol. The final two steps of ethanol production are mediated by a bifunctional enzyme, AdhE, and this enzyme is a frequent target of mutations in strains engineered for increased ethanol production. Paradoxically, these mutations increase ethanol production by eliminating the activity of one domain of the AdhE enzyme (the ADH domain). This provides additional support for a redox-imbalance theory of alcohol tolerance, which challenges the prevailing hypothesis that alcohol tolerance is associated with cell membrane effects.
59 BASIC BIOLOGICAL SCIENCES↗
Induced Ferromagnetism in Epitaxial Uranium Dioxide Thin Films
Abstract Actinide materials have various applications that range from nuclear energy to quantum computing. Most current efforts have focused on bulk actinide materials. Tuning functional properties by using strain engineering in epitaxial thin films is largely lacking. Using uranium dioxide (UO 2 ) as a model system, in this work, the authors explore strain engineering in actinide epitaxial thin films and investigate the origin of induced ferromagnetism in an antiferromagnet UO 2 . It is found that UO 2+ x thin films are hypostoichiometric ( x <0) with in‐plane tensile strain, while they are hyperstoichiometric ( x >0) with in‐plane compressive strain. Different from strain engineering in non‐actinide oxide thin films, the epitaxial strain in UO 2 is accommodated by point defects such as vacancies and interstitials due to the low formation energy. Both epitaxial strain and strain relaxation induced point defects such as oxygen/uranium vacancies and oxygen/uranium interstitials can distort magnetic structure and result in magnetic moments. This work reveals the correlation among strain, point defects and ferromagnetism in strain engineered UO 2+ x thin films and the results offer new opportunities to understand the influence of coupled order parameters on the emergent properties of many other actinide thin films.
36 MATERIALS SCIENCE↗
Genetically engineered Pseudomonas strains capable of metabolizing ethylene glycol and its metabolic intermediates
Presented herein are genetically engineered Pseudomonas strains capable of metabolizing ethylene glycol and producing polyhydroxyalkanoates.
Beckham, Gregg Tyler↗
Advances in engineering algae for biofuel production
While algae demonstrate potential as a sustainable fuel source, low productivities limit the economic realization of algal biofuels. High-throughput strain engineering, omics-informed genome-scale modeling, and microbiome engineering are key technologies for enabling algal biofuels. High-throughput strain engineering efforts generate improved traits, including high biomass productivity and lipid content, in diverse algal species. Genome-scale models, constructed with the aid of omics data, provide insight into metabolic limitations and guide rational algal strain engineering efforts. As outdoor cultivation systems introduce exogenous organisms, microbiome engineering seeks to eliminate harmful organisms and introduce beneficial species. In conclusion, optimizing algal biomass production and lipid content using these technologies may overcome the productivity barrier for the commercialization of algal biofuels.
09 BIOMASS FUELS↗
Engineered yeast strains enabling anaerobic xylose fermentation decoupled from microbial growth
The present invention relates to materials and methods for the production of ethanol. More particularly, the present invention provides genetically modified strains of Saccharomyces cerevisiae exhibiting decreased level of BCY1 protein activity and capable of anaerobic fermentation of xylose into ethanol without the need for cell growth. Also provided are methods of using such genetically engineered yeast strains for improved anaerobic xylose fermentation in the yeast for industrial-scale production of various fuels, chemical feedstocks, and synthetic polymers.
Myers, Kevin S.↗
Engineering Clostridium cellulovorans for highly selective n ‐butanol production from cellulose in consolidated bioprocessing
Abstract Cellulosic n ‐butanol from renewable lignocellulosic biomass has gained increased interest. Previously, we have engineered Clostridium cellulovorans , a cellulolytic acidogen, to overexpress the bifunctional butyraldehyde/butanol dehydrogenase gene adh E2 from C. acetobutylicum for n ‐butanol production from crystalline cellulose. However, butanol production by this engineered strain had a relatively low yield of approximately 0.22 g/g cellulose due to the coproduction of ethanol and acids. We hypothesized that strengthening the carbon flux through the central butyryl‐CoA biosynthesis pathway and increasing intracellular NADH availability in C. cellulovorans adh E2 would enhance n ‐butanol production. In this study, thiolase ( thl A CA ) from C. acetobutylicum and 3‐hydroxybutyryl‐CoA dehydrogenase ( hbd CT ) from C. tyrobutyricum were overexpressed in C. cellulovorans adh E2 to increase the flux from acetyl‐CoA to butyryl‐CoA. In addition, ferredoxin‐NAD(P) + oxidoreductase ( fnr ), which can regenerate the intracellular NAD(P)H and thus increase butanol biosynthesis, was also overexpressed. Metabolic flux analyses showed that mutants overexpressing these genes had a significantly increased carbon flux toward butyryl‐CoA, which resulted in increased production of butyrate and butanol. The addition of methyl viologen as an electron carrier in batch fermentation further directed more carbon flux towards n ‐butanol biosynthesis due to increased reducing equivalent or NADH. The engineered strain C. cellulovorans adh E2‐ fnr CA ‐ thl A CA ‐ hbd CT produced n ‐butanol from cellulose at a 50% higher yield (0.34 g/g), the highest ever obtained in batch fermentation by any known bacterial strain. The engineered C. cellulovorans is thus a promising host for n ‐butanol production from cellulosic biomass in consolidated bioprocessing.
Bao, Teng↗
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↗
Metallization of diamond
Experimental discovery of ultralarge elastic deformation in nanoscale diamond and machine learning of its electronic and phonon structures have created opportunities to address new scientific questions. Can diamond, with an ultrawide bandgap of 5.6 eV, be completely metallized, solely under mechanical strain without phonon instability, so that its electronic bandgap fully vanishes? Through first-principles calculations, finite-element simulations validated by experiments, and neural network learning, we show here that metallization/demetallization as well as indirect-to-direct bandgap transitions can be achieved reversibly in diamond below threshold strain levels for phonon instability. We identify the pathway to metallization within six-dimensional strain space for different sample geometries. We also explore phonon-instability conditions that promote phase transition to graphite. These findings offer opportunities for tailoring properties of diamond via strain engineering for electronic, photonic, and quantum applications.
36 MATERIALS SCIENCE↗
ABF Industry Engagement Lab Call with Danimer Scientific
This Agile BioFoundry Directed Funding Opportunity project with Danimer Scientific focuses on the development of a strain and a corresponding bioprocess to convert bio-based feedstocks to mixed composition polyhydroxyalkanoates (PHAs). Danimer Scientific produces PHAs today at industrial scale in proprietary strains and for many applications where bio-based, biodegradable materials are advantaged. The project team consists of NREL to lead the strain engineering efforts, PNNL to conduct systems biology experiments that will inform further strain engineering, and Danimer to conduct bioprocess development and materials development. To date, we have on-boarded Danimer strains and demonstrated successful engineering thereof. We anticipate conducting systems biology studies in Spring 2023. Overall, the impact of this DFO project could be improved material properties accessed through the Design-Build-Test-Learn cycle for designer PHA production.
bio-based feedstocks↗