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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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Structural and biochemical characterization of the class II fructose-1,6-bis-phosphatase from Franci
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Structural and biochemical analysis of Bacillus anthracis prephenate dehydrogenase reveals an unusua
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Retrospective analysis of biochemical limitations to photosynthesis in 49 species: C 4 crops appear still adapted to pre‐industrial atmospheric [ CO 2 ]
Abstract Leaf CO 2 uptake ( A ) in C 4 photosynthesis is limited by the maximum apparent rate of PEPc carboxylation ( V pmax ) at low intercellular [CO 2 ] ( c i ) with a sharp transition to a c i ‐saturated rate ( V max ) due to co‐limitation by ribulose‐1:5‐bisphosphate carboxylase/oxygenase (Rubisco) and regeneration of PEP. The response of A to c i has been widely used to determine these two parameters. V max and V pmax depend on different enzymes but draw on a shared pool of leaf resources, such that resource distribution is optimized, and A maximized, when V max and V pmax are co‐limiting. We collected published A / c i curves in 49 C 4 species and assessed variation in photosynthetic traits between phylogenetic groups, and as a function of atmospheric [CO 2 ]. The balance of V max ‐ V pmax varied among evolutionary lineages and C 4 subtypes. Operating A was strongly V max ‐limited, such that re‐allocation of resources from V pmax towards V max was predicted to improve A by 12% in C 4 crops. This would not require additional inputs but rather altered partitioning of existing leaf nutrients, resulting in increased water and nutrient‐use efficiency. Optimal partitioning was achieved only in plants grown at pre‐industrial atmospheric [CO 2 ], suggesting C 4 crops have not adjusted to the rapid increase in atmospheric [CO 2 ] of the past few decades.
Biochemical and structural insights into SARS-CoV-2 polyprotein processing by Mpro
SARS-CoV-2, a human coronavirus, is the causative agent of the COVID-19 pandemic. Its genome is translated into two large polyproteins subsequently cleaved by viral papain-like protease and main protease (Mpro). Polyprotein processing is essential yet incompletely understood. We studied Mpro-mediated processing of the nsp7-11 polyprotein, whose mature products include cofactors of the viral replicase, and identified the order of cleavages. Integrative modeling based on mass spectrometry (including hydrogen-deuterium exchange and cross-linking) and x-ray scattering yielded a nsp7-11 structural ensemble, demonstrating shared secondary structural elements with individual nsps. The pattern of cross-links and HDX footprint of the C145A Mpro and nsp7-11 complex demonstrate preferential binding of the enzyme active site to the polyprotein junction sites and additional transient contacts to help orient the enzyme on its substrate for cleavage. Last, proteolysis assays were used to characterize the effect of inhibitors/binders on Mpro processing/inhibition using the nsp7-11 polyprotein as substrate.
Genetic and biochemical characterization of a radical SAM enzyme required for post-translational glutamine methylation of methyl-coenzyme M reductase
ABSTRACT Methyl-coenzyme M reductase (MCR), the key catalyst in the anoxic production and consumption of methane, contains an unusual 2-methylglutamine residue within its active site. In vitro data show that a B12-dependent radical SAM (rSAM) enzyme, designated MgmA, is responsible for this post-translational modification (PTM). Here, we show that two different MgmA homologs are able to methylate MCR in vivo when expressed in Methanosarcina acetivorans , an organism that does not normally possess this PTM. M. acetivorans strains expressing MgmA showed small, but significant, reductions in growth rates and yields on methylotrophic substrates. Structural characterization of the Ni(II) form of Gln-methylated M. acetivorans MCR revealed no significant differences in the protein fold between the modified and unmodified enzyme; however, the purified enzyme contained the heterodisulfide reaction product, as opposed to the free cofactors found in eight prior M. acetivorans MCR structures, suggesting that substrate/product binding is altered in the modified enzyme. Structural characterization of MgmA revealed a fold similar to other B12-dependent rSAMs, with a wide active site cleft capable of binding an McrA peptide in an extended, linear conformation. IMPORTANCE Methane plays a key role in the global carbon cycle and is an important driver of climate change. Because MCR is responsible for nearly all biological methane production and most anoxic methane consumption, it plays a major role in setting the atmospheric levels of this important greenhouse gas. Thus, a detailed understanding of this enzyme is critical for the development of methane mitigation strategies.
Strategies for the production of biochemicals in bioenergy crops
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From the bench to the reactor: engineered filamentous fungi for biochemical and biomaterial production
Filamentous fungi can convert a wide variety of naturally occurring chemical compounds, including organic biomass and waste streams, into a range of products. They have long been used for industrial organic acid production and food preparation. In this review, we will discuss production of products such as organic acids, lipids, small molecules, enzymes, materials, and foods, and highlight advances in metabolic and protein engineering, including CRISPR-Cas9-mediated strain improvements. We discuss to what extent these products are already being made on a commercial scale, as well as what is still required to make certain promising concepts industrially and commercially relevant. Despite significant progress, the systematic application of synthetic biology to filamentous fungi remains in its infancy, with many opportunities for discovery and innovation as new strains and genetic tools are developed. The integration of fungal biotechnology into circular and bio-based economies promises to address critical challenges in waste management, resource sustainability, and the development of new materials for terrestrial and extraterrestrial applications, but requires further developments in genetic engineering and process design.
Biophysical and biochemical studies support TP0094 as a phosphotransacetylase in an acetogenic energy-conservation pathway in Treponema pallidum
The mechanisms of energy generation and carbon-source utilization in the syphilis spirochete Treponema pallidum have remained enigmatic despite complete genomic sequence information. Whereas the bacterium harbors enzymes for glycolysis, the apparatus for more efficient use of glucose catabolites, namely the citric-acid cycle, is apparently not present. Yet, the organism’s energy needs likely exceed the modest output from glycolysis alone. Recently, building on our structure-function studies of T . pallidum lipoproteins, we proposed a “flavin-centric” metabolic lifestyle for the organism that partially resolves this conundrum. As a part of the hypothesis, we have proposed that T . pallidum contains an acetogenic energy-conservation pathway that catabolizes D-lactate, yielding acetate, reducing equivalents for the generation and maintenance of chemiosmotic potential, and ATP. We already have confirmed the D-lactate dehydrogenase activity in T . pallidum necessary for this pathway to operate. In the current study, we focused on another enzyme ostensibly involved in treponemal acetogenesis, phosphotransacetylase (Pta). This enzyme is putatively identified as TP0094 and, in this study, we determined a high-resolution (1.95 Å) X-ray crystal structure of the protein, finding that its fold comports with other known Pta enzymes. Further studies on its solution behavior and enzyme activity confirmed that it has the properties of a Pta. These results are consistent with the proposed acetogenesis pathway in T . pallidum , and we propose that the protein be referred to henceforth as TpPta.
Aligned FTICR-MS, Respiration, and Biochemical Transformation Data from Columbia River Sediment Incubations Associated with: “Carbon Limitation Leads to Thermodynamic Regulation of Aerobic Metabolism”
Columbia River hyporheic zone sediments from the Hanford Site 300 Area in eastern Washington were incubated in a full factorial design with different organic matter (OM) amendments. The aim of the experiment was to test the influence of OM thermodynamics on aerobic respiration across different organic carbon pools and concentrations. This dataset is comprised of (1) a csv with high resolution characterization of dissolved organic matter via 12 Tesla Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) analyzed through the Environmental Molecular Sciences Laboratory (EMSL; https://www.pnnl.gov/environmental-molecular-sciences-laboratory), (2) a csv with sample IDs, replicates, amendments, dissolved oxygen (DO) measurements, and sampling time points, (3) a csv with sample IDs, replicates, respiration rates, FTICR summary metrics, and relative abundance of chemical classes; and (4) a csv with the number of chemical transformations in each sample replicate (microcosm). The data are associated with the publication “Carbon Limitation Leads to Thermodynamic Regulation of Aerobic Metabolism” published in ES&T Letters (Garayburu-Caruso et al., 2020). Please use the data package’s DOI to cite the data package. We ask that you acknowledge the U.S. Department of Energy (DOE) Biological and Environmental Research (BER) Subsurface Biogeochemical Research (SBR) program when using the data. All data are free to be used for any purpose, such as for manuscripts, presentations, and grant proposals. There is no obligation to include data package authors as co-authors.
Biochemical integration of metabolic networks critical for energy transformation in Chlamydomonas reinhardtii
The project involved examining the importance of various aspects of photochemical quenching of photosynthetic electron transport. One focus of the project was the AOX or alternative oxidase of the mitochondria and it role in survival during high light conditions.
Microalgae Conversion to Biofuels and Biochemical via Sequential Hydrothermal Liquefaction (SEQHTL) and Bioprocessing: 2020 State of Technology
A preliminary techno-economic analysis (TEA) was developed for the fiscal year 2020 state of technology (SOT) assessment to evaluate the benefits and risks for a large-scale microalga hydrothermal liquefaction (HTL) system based on most recent testing results. The focus of the study is directed toward the conversion system, which consists of five processes: two-stage sequential HTL (SEQHTL), biocrude upgrading to final fuels, bioprocessing for co-product generation, hydrogen generation, and steam cycle. In this system, algae biomass with corn stover supplement during the lower algae productivity seasons (winter, fall, and spring) to match the maximum algae seasonal production rate in summer is employed to maintain a constant plant capacity in all the seasons. Algae only (summer season) or algae/corn stover blended feedstock (other seasons) are sent to a two-stage SEQHTL process. In stage I, the carbohydrates in the feedstock are extracted and separated from the residual solid. The residual solid from stage I is further converted to biocrude in the SEQHTL stage II step. The biocrude is upgraded to final fuel products in an upgrading process. The extract stream from HTL stage I is sent to the bioprocessing section for co-product generation via fermentation of carbohydrate. Lactic acid (LA) is assumed to be the co-product based on current bioprocessing testing results.
Resolving Conflicting Physical and Biochemical Feedbacks to Climate in Response to Long-Term Warming
The goal of the research was to increase our understanding of the microbial mechanisms that control soil organic matter decay in the context of a changing climate. We hypothesized that a major source of carbon respired after long-term soil warming is recalcitrant soil C mineralized by microbes. We found that long-term warming was associated with decreased fungal communities but not bacterial communities, with bacterial communities in organic horizon soils significantly affected by warming. Molecular analysis indicated that this community shift was towards a more oligotrophic community, consistent with previously observed decreased in soil organic matter quality and quantity. We further hypothesized that low labile C resulting from long-term warming has selected for a microbial community that is better able to mineralize recalcitrant C. Analysis of soil communities and individual isolates physiology showed that long-term warming caused bacteria to have increased potential lignolytic activitiy as well as increased carbohydrate degradation potential. This increased ability to degrade recalcitrant soil organic matter is suggested as a mechanism for accelerated soil carbon loss with long-term warming. Soil warming was shown to have little change in transcriptional activity or proteins levels of the enzymes related to recalcitrant C, and little change in the temperature sensitivity of enzyme activity.
Supply Chain Sustainability Analysis of Renewable Hydrocarbon Fuels via Indirect Liquefaction, Hydrothermal Liquefaction, Combined Algal Processing, and Biochemical Conversion: Update of the 2021 State-of-Technology Cases
The Department of Energy’s (DOE) Bioenergy Technologies Office (BETO) aims to develop and deploy technologies to transform renewable biomass resources into commercially viable, high-performance biofuels, bioproducts, and biopower through public and private partnerships. BETO and its national laboratory teams conduct in-depth techno-economic assessments (TEA) of biomass feedstock supply and logistics and conversion technologies to produce biofuels. There are two general types of TEAs: A design case outlines a target case (future projection) for a particular biofuel pathway. It informs R&D priorities by identifying areas in need of improvement, tracks sustainability impact of R&D, and provides goals and benchmarks against which technology progress is assessed. A state of technology (SOT) analysis assesses progress within and across relevant technology areas based on actual results at current experimental scales relative to technical targets and cost goals from design cases, and includes technical, economic, and environmental criteria as available.
Supply Chain Sustainability Analysis of Renewable Hydrocarbon Fuels via Indirect Liquefaction, Hydrothermal Liquefaction, Combined Algal Processing, and Biochemical Conversion: Update of the 2021 State-of-Technology Cases
The Department of Energy’s (DOE) Bioenergy Technologies Office (BETO) aims to develop and deploy technologies to transform renewable biomass resources into commercially viable, high-performance biofuels, bioproducts, and biopower through public and private partnerships. BETO and its national laboratory teams conduct in-depth techno-economic assessments (TEA) of biomass feedstock supply and logistics and conversion technologies to produce biofuels. There are two general types of TEAs: A design case outlines a target case (future projection) for a particular biofuel pathway. It informs R&D priorities by identifying areas in need of improvement, tracks sustainability impact of R&D, and provides goals and benchmarks against which technology progress is assessed. A state of technology (SOT) analysis assesses progress within and across relevant technology areas based on actual results at current experimental scales relative to technical targets and cost goals from design cases, and includes technical, economic, and environmental criteria as available.
Propulsion of synthetic protocells and coacervates driven by biochemical catalysis
An important area in the design of biomolecular materials is the mimicry of cellular function through the assembly of molecular components into synthetic cells, or protocells. Through compartmentalization and subsequent evolution, biological cells have achieved the goals of specificity, amplification, and response. By assembling cell-like structures that mimic the organization and size of a natural cell but that incorporate novel components and respond to synthetic triggers, we can extend their capabilities beyond what is currently achievable in biology. For applications in energy, these include the ability to convert chemical to mechanical energy, and to enable the response of sensors and responders once a threshold has been reached. This technical report summarizes progress made on this project as of Dec 31, 2023.
Biochemical Conversion of Herbaceous Biomass to Renewable Diesel: Biorefinery Marginal Air Quality Impacts and Comparison to Feedstock Production
This study assesses the air quality impacts of an advanced biorefinery that produces renewable diesel blendstock (RDB) from lignocellulosic biomass via aerobic respiration (Davis et al. 2022) by estimating fine particulate matter (PM2.5) impacts from biorefinery emissions. It continues a prior analysis that used a geospatial assessment to identify source regions for biomass feedstocks and studied the impact of feedstock production emissions on air quality (Thind et al. 2022). Thind et al. (2022) identified RDB biorefineries that can use corn stover feedstocks of 2,000; 5,200; and 9,100 dry metric tons per day (DMT/day), based in Iowa, and suggested 7 unique counties can serve as hosts for a biorefinery that draws biomass feedstock from neighboring counties. Given 13 unique county-biorefinery size combinations and two waste lignin end uses at the biorefinery (lignin as a fuel for electricity generation and lignin for pellet production), the air-quality-related sustainability aspects of each of these 26 scenarios are assessed by estimating the annual average impacts of biorefinery emissions on the dispersion and formation of secondary PM2.5 in the atmosphere using a novel reduced-complexity air quality model called the Intervention Model for Air Pollution (InMAP). The 26 biorefinery design combinations help capture how a biorefinery's emissions of air pollutants and their resulting impact on local and regional air quality are influenced by the magnitude of production scale, lignin utilization strategy, and location of a proposed biorefinery. Methods developed in Thind et al. (2022) are applied to estimate the constraints on primary PM2.5 and secondary PM2.5 precursor emissions based on compliance with U.S. Environmental Protection Agency's (EPA's) annual primary National Ambient Air Quality Standard (NAAQS) of PM2.5 (i.e.12.0 micrograms per cubic meter (microgram/m3)) at downwind receptors of a biorefinery. Incremental PM2.5 concentrations caused by the emission of biorefining corn stover into RDB are assessed and compared to those of corn stover production. To illuminate which upstream supply chain stage of renewable diesel production contributes most to air quality impacts, marginal PM2.5 concentrations are compared between both stages at multiple downwind air quality monitor locations. In addition, through a hotspot analysis, we identify the primary contributing factors of emissions within the feedstock production and biorefinery stage operations. In doing so, we provide insights for improving the air pollutant emission-related sustainability of advanced lignocellulosic biofuel production.