Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “biochemicals”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 487 records · Page 27
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Phylogenetics-based identification and characterization of a superior 2,3-butanediol dehydrogenase for Zymomonas mobilis expression

Abstract Background Zymomonas mobilis has recently been shown to be capable of producing the valuable platform biochemical, 2,3-butanediol (2,3-BDO). Despite this capability, the production of high titers of 2,3-BDO is restricted by several physiological parameters. One such bottleneck involves the conversion of acetoin to 2,3-BDO, a step catalyzed by 2,3-butanediol dehydrogenase (Bdh). Several Bdh enzymes have been successfully expressed in Z. mobilis, although a highly active enzyme is yet to be identified for expression in this host. Here, we report the application of a phylogenetic approach to identify and characterize a superior Bdh, followed by validation of its structural attributes using a mutagenesis approach. Results Of the 11 distinct bdh genes that were expressed in Z. mobilis, crude extracts expressing Serratia marcescens Bdh ( Sm Bdh) were found to have the highest activity (8.89 µmol/min/mg), when compared to other Bdh enzymes (0.34–2.87 µmol/min/mg). The Sm Bdh crystal structure was determined through crystallization with cofactor (NAD + ) and substrate (acetoin) molecules bound in the active site. Active Sm Bdh was shown to be a tetramer with the active site populated by a Gln247 residue contributed by the diagonally opposite subunit. Sm Bdh showed a more extensive supporting hydrogen-bond network in comparison to the other well-studied Bdh enzymes, which enables improved substrate positioning and substrate specificity. This protein also contains a short α6 helix, which provides more efficient entry and exit of molecules from the active site, thereby contributing to enhanced substrate turnover. Extending the α6 helix to mimic the lower activity Enterobacter cloacae ( Ec Bdh) enzyme resulted in reduction of Sm Bdh function to nearly 3% of the total activity. In great contrast, reduction of the corresponding α6 helix of the Ec Bdh to mimic the Sm Bdh structure resulted in ~ 70% increase in its activity. Conclusions This study has demonstrated that Sm Bdh is superior to other Bdhs for expression in Z. mobilis for 2,3-BDO production. Sm Bdh possesses unique structural features that confer biochemical advantage to this protein. While coordinated active site formation is a unique structural characteristic of this tetrameric complex, the smaller α6 helix and extended hydrogen network contribute towards improved activity and substrate promiscuity of the enzyme.

09 BIOMASS FUELS↗
DOE OSTI2025

The anaerobic fungus Neocallimastix californiae shifts metabolism and produces melanin in response to lignin-derived aromatic compounds

Biological deconstruction of lignocellulose for sustainable chemical production offers an opportunity to harness evolutionarily specialized enzymes and organisms for industrial bioprocessing. While hydrolysis of cellulose and hemicellulose by CAZymes yields fermentable sugars, ligninolysis releases a heterogeneous mix of aromatic compounds that likely play a crucial role in shaping microbial communities and microbial metabolism. Here, we interrogated the metabolomic and transcriptomic response of a lignocellulolytic anaerobic fungus, Neocallimastix californiae, to a heterogeneous mixture of aromatic compounds derived from lignin. Through exposing the fungus to both a concentration it might experience in its native environment and an elevated concentration of alkaline lignin, we observe that N. californiae transforms vanillin and that supplying alkaline lignin at 0.125 g/L, alongside cellulose, enhances the growth and polysaccharide-degrading activity of N. californiae. Altogether, our results further suggest that vanillin consumption, increased polymer-degrading activity, increased metabolic activity, and transcriptomic remodeling of amino acid synthesis genes all coincide with increased melanin production by fungal cells. These observations challenge previous notions that aromatics from lignocellulose only inhibit the growth and polymer deconstruction capabilities of the biomass-degrading anaerobic fungi (Neocallimastigomycetes). This study demonstrates that anaerobic fungi have a complex relationship with aromatic chemicals derived from lignin and hemicellulose and shift their metabolism in response to the addition of lignocellulose-derived aromatics to their growth medium. Further, as no known pathways for the biochemical transformation of aromatics were detected in these organisms despite observed transcriptome remodeling in the presence of aromatics, we suggest they might encode novel biochemical routes for scavenging amino acid building blocks from aromatic monomers derived from hemicellulose side chains and lignin.

Anaerobic fungi↗
DOE OSTI2021

Granick revisited: Synthesizing evolutionary and ecological evidence for the late origin of bacteriochlorophyll via ghost lineages and horizontal gene transfer

Photosynthesis—both oxygenic and more ancient anoxygenic forms—has fueled the bulk of primary productivity on Earth since it first evolved more than 3.4 billion years ago. However, the early evolutionary history of photosynthesis has been challenging to interpret due to the sparse, scattered distribution of metabolic pathways associated with photosynthesis, long timescales of evolution, and poor sampling of the true environmental diversity of photosynthetic bacteria. Here, we reconsider longstanding hypotheses for the evolutionary history of phototrophy by leveraging recent advances in metagenomic sequencing and phylogenetics to analyze relationships among phototrophic organisms and components of their photosynthesis pathways, including reaction centers and individual proteins and complexes involved in the multi-step synthesis of (bacterio)-chlorophyll pigments. We demonstrate that components of the photosynthetic apparatus have undergone extensive, independent histories of horizontal gene transfer. This suggests an evolutionary mode by which modular components of phototrophy are exchanged between diverse taxa in a piecemeal process that has led to biochemical innovation. We hypothesize that the evolution of extant anoxygenic photosynthetic bacteria has been spurred by ecological competition and restricted niches following the evolution of oxygenic Cyanobacteria and the accumulation of O 2 in the atmosphere, leading to the relatively late evolution of bacteriochlorophyll pigments and the radiation of diverse crown group anoxygenic phototrophs. This hypothesis expands on the classic “Granick hypothesis” for the stepwise evolution of biochemical pathways, synthesizing recent expansion in our understanding of the diversity of phototrophic organisms as well as their evolving ecological context through Earth history.

58 GEOSCIENCES↗
DOE OSTI2020

Novel Microbial Based Enzymatic CO 2 Fixation Mechanisms

The broad, long term goal of the research is to provide insight into the mechanism of novel carboxylation reactions catalyzed by enzymes involved in bacterial alkene, ketone, and epoxide metabolism. Novel convergent pathways in the model microorganism Xanthobacter autotrophicus have been described in which epoxides produced by alkene oxidation and ketones produced by the oxidation of alcohols are further carboxylated and utilized in energy yielding pathways. Both alkene/epoxide and alcohol/ketone pathways involve distinct carboxylases with unique molecular properties and cofactor requirements that represent alternative mechanisms of CO 2 fixation. The main focus and aims of this project is to provide structural basis for the mechanistic understanding of the reactions catalyzed by 2-ketopropyl coenzyme M oxidoreductase / carboxylase and acetone carboxylase, the terminal steps in the convergent pathways of alkene/epoxide and alcohol ketone metabolism in X. autotrophicus strain Py2. Interestingly, coenzyme M (CoM), the simplest known organic coenzyme, has been shown to have a central role in the pathway of alkene/epoxide carboxylation. Prior to this discovery CoM was thought only to be involved in methanogenesis in archaea. In addition to the carboxylation mechanisms, we are examining the enzymology of the biosynthesis of CoM in bacteria and we have already determined that it is biochemically distinct from that of CoM synthesized by methanogens. The proposed studies will reveal new and unique insights into CO 2 fixation pathways and carboxylation chemistry. We are utilizing a multidisciplinary approach involving kinetic studies, site-specific amino acid substitution studies, and the determination of high-resolution structures of enzymes in the presence of substrate analogs and mechanism base inhibitors to ascertain information concerning the biochemical mechanisms of enzyme catalyzed reactions. Within the context of the mission of the Department of Energy and the core activities of the Energy Biosciences, the results obtained in the study will reveal new insights into these novel carboxylation reactions and will provide the basis for the comparison of the mechanism of these interesting enzymes to other well-characterized biological mechanisms for CO 2 fixation and carboxylation. Knowledge concerning the mechanism of these enzymes provides the basis for an increased fundamental understanding of carboxylation chemistry that could contribute to future mechanisms for CO 2 capture and fixation and, in turn, to mitigating the effects of increasing concentrations of CO 2 on global climate change.

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

Ecosystems and Networks Integrated with Genes and Molecular Assemblies (ENIGMA): Component 5: Imaging Protein Conformations, Shapes & Assemblies in Solution & Administration project (Final Scientific/Technical Report, Subcontract No. 6974584)

We set ambitious goals to examine microorganism communities and measure both their chemical input and output as a read out of specific biochemical activity. These scientific goals are driving the development of sophisticated algorithms to analyze large amounts of experimental measurements made using high throughput technologies to explain and predict how the environment influences biological function at multiple scales and how the microbial systems in tum modify the environment. By examining how bacteria communities rely on symbiotic metabolic relationships for survival and reproductive success, and how these relationships consequently affect their biochemical capabilities. This was accomplished using state-of-the-art mass spectrometry-based methods, and metabolic fingerprinting approaches with a high degree of chemical specificity and sensitivity. During this period the original effort transitioned and was consolidated into what is now ENIGMA, the efforts on technology development expanded to include more untargeted metabolomics and its application to organisms on a systems level.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Dissection of Grass Cell Wall Lignin Formation and their Associated Dirigent Protein

This Final Report describes work underway to establish why monocot (e.g. grasses) lignins are more readily (bio)degradable than their woody gymnosperm, angiosperm, and fern counterparts. Our hypothesis is that monocot specific dirigent protein (DP) sub-families are wholly or partly involved in generating these more readily (bio)degradable lignins. Three approaches are underway: metabolomics and lignin analyses of stem and leaf tissues of the grass, Brachypodium; Crispr/Cas9 gene editing of monocot specific DP sub-families in this species, and recombinant protein expression of Brachypodium’s 44 DPs. Metabolomic and lignin analyses were completed for 6 and 8 week old Brachypodium in order to establish the molecular diversity of its largely phenolic metabolites: Crispr/Cas9 gene editing has also been done on specific DPs known to be expressed in lignifying stems, and T 2 generation plant lines are now being generated, prior to establishing the effects on lignin composition and content; in the recombinant DP work (which addresses establishing the biochemical function of the monocot specific DPs and other DPOs as needed), all 44 constructs have been generated (in collaboration with DOE JGI) and are being systematically expressed in either E. coli or yeast (Pichia sp.) for future studies. Future work will be directed towards bringing the current studies to completion, and in establishing the biochemical basis as to how these more readily (bio)degradable lignins are generated/assembled.

(bio)degradability↗
DOE OSTI2023

Ecosystems and Networks Integrated with Genes and Molecular Assemblies (ENIGMA): Integrating Metabolomics into Environmental Systems Biology

Our research endeavors entail ambitious objectives to explore the communities of microorganisms and quantify their chemical input and output to determine specific biochemical activity. To achieve these scientific aims, we are creating advanced algorithms to scrutinize extensive experimental data produced through high-throughput technologies, enabling us to elucidate how biological functions are influenced by environmental factors on various scales, and how microbial systems alter their surroundings. By studying the metabolic interdependence of bacterial communities for their survival and reproductive prosperity, we can gain insights into their biochemical capabilities. To accomplish this, we employed cutting-edge mass spectrometry-based techniques and metabolic fingerprinting methods, which offer high chemical specificity and sensitivity. As our efforts progressed, the project evolved into ENIGMA, encompassing a broader range of technology development, including untargeted metabolomics and its implementation for system-level organism analysis.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Disruptive Technology for Carbon Negative Commodity Chemicals

This project was designed to develop an economically attractive process for the carbon negative production of the commodity biochemical succinic acid. To compete against petroleum derived biochemicals, the process must deliver high raw material conversion efficiency and high volumetric productivity to reduce both recurring and capital-related costs, respectively. The proposed process introduces additional electrons sourced from hydrogen into the biosynthetic pathway so that the carbon from two CO2 molecules can be combined with each glucose to significantly increase succinic acid yields. The process also uses ultrafiltration to continuously remove the product from the bioreactor to avoid product inhibition and extend the productive life of the cell extract. Genetic deletions and specific enzyme removal during extract preparation more efficiently direct both atomic and electronic resources toward product formation. A preliminary technoeconomic analysis indicates that these process innovations made possible by cell-free production will enable large scale production with attractive ROI and profitability. This two-year project provided some 29 distinct insights, analytical advances, and process improvements that resulted in a demonstration of process feasibility. However, an estimated two to three years of additional development will be required to achieve convincing pilot scale demonstrations that will motivate large scale investments.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Neutrons in Structural Biology: Challenges and Opportunities (Workshop Report)

Gaining a thorough understanding of biological systems requires building our knowledge about biological processes from the level of atoms and electrons, and up to whole organisms. Such comprehensive knowledge will allow for a predictive understanding of complex biological systems behavior. It will guide us in the design and development of novel therapeutics and vaccines to tackle existing health threats and to prepare for future pandemics, and it will provide information necessary to create new biomaterials and bio-inspired technologies through manipulation of biological macromolecules, their assemblies, single cells and even microorganisms. Reaching these goals will require a synergistic combination of multiple experimental techniques with molecular calculations and predictive simulations, and the design and development of new techniques and capabilities that bridge current knowledge and technology gaps. Neutron scattering provides unique information about the biomacromolecular structure and function and can play a major role in achieving these goals. A workshop was held to engage the scientific community in identifying pressing challenges in biochemistry, structural biology, enzymology and structure-guided drug design not solved with the current neutron scattering technologies or utilizing other structural biology techniques such as X-ray crystallography, NMR, and cryo-EM. The workshop brought together structural biology, biochemistry and computational experts, as well as early career researchers and students, creating a forum for discussing scientific advancement and collaboration. The workshop included a one-day satellite training workshop where graduate students and postdoctoral researchers were educated in the application of neutron crystallography and small-angle scattering in structural biology. Furthermore, the Instrument Scientific Advisory Board (ISAB) for the development of a macromolecular neutron diffractometer at ORNL’s Second Target Station was introduced at the workshop. The major outcome was that neutrons can provide atomic-level understanding of biomacromolecular structure, function and dynamics which is of paramount importance for addressing the identified challenges. Neutron crystallography, in particular, can resolve long-standing biochemical issues regarding enzyme function by delineating the underlying chemistry and can have a major impact on the design of small-molecule therapeutics, especially in combination with molecular computation (quantum chemistry and molecular dynamics simulations) and the emerging artificial intelligence (AI)-assisted drug design technologies. The unique properties of neutrons, including their high sensitivity to hydrogen and their non-destructive nature, make them ideal probes of biological matter. There is a palpable need in the scientific community to expand and enhance the impact of neutron sciences on biology. Neutron crystallography is the only structural biology method capable of determining positions of all hydrogen atoms in proteins, nucleic acids and their complexes at near-physiological temperatures and of unstable species at cryogenic temperatures. Moreover, neutron analysis is non-ionizing, non-destructive and does not perturb the structure or redox chemistry of active site metal centers and clusters in proteins, which can be invaluable for studying radiation-sensitive metalloprotein complexes. Further, neutron energies used in scattering applications are similar to atomic motions, permitting neutron spectroscopies to characterize the dynamics of biomacromolecules on the picosecond to microsecond timescales. The different sensitivities of neutrons to protium (H) and deuterium (D) isotopes of hydrogen allow enhanced visibility of specific parts of biological complexes through isotopic labeling. The impact of neutrons will be most powerful when neutron scattering is combined with complementary experimental techniques that use photons and electrons, and with high-performance computing. The interconnection and mutuality of the experimental and theoretical capabilities will drive discoveries in biological and health sciences to generate more complete picture of complex biological systems. The major limitation in the field of biological neutron crystallography has been signal-to-noise, demanding large samples that are difficult to produce for the majority of biomacromolecules and limiting the applicability of this technique in biological sciences. A neutron crystallography instrument at the Second Target Station will revolutionize biological science with neutrons by engaging a large scientific community of structural biologists, enabling successful neutron diffraction experiments from radically smaller biomacromolecular crystals, resolving unanswered biochemical questions, and meaningfully contributing to rational drug design. The meeting highlighted 10 grand challenges that will be addressed with this advanced capability over the next decade and beyond, and the recommendations required to help address them are given below.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Workflow for High-throughput Screening of Enzyme Mutant Libraries Using Matrix-assisted Laser Desorption/Ionization Mass Spectrometry Analysis of Escherichia coli Colonies

High-throughput molecular screening of microbial colonies and DNA libraries are critical procedures that enable applications such as directed evolution, functional genomics, microbial identification, and creation of engineered microbial strains to produce high-value molecules. A promising chemical screening approach is the measurement of products directly from microbial colonies via optically guided matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Measuring the compounds from microbial colonies bypasses liquid culture with a screen that takes approximately 5 s per sample. We describe a protocol combining a dedicated informatics pipeline and sample preparation method that can prepare up to 3,000 colonies in under 3 h. The screening protocol starts from colonies grown on Petri dishes and then transferred onto MALDI plates via imprinting. The target plate with the colonies is imaged by a flatbed scanner and the colonies are located via custom software. The target plate is coated with MALDI matrix, MALDI-MS analyzes the colony locations, and data analysis enables the determination of colonies with the desired biochemical properties. This workflow screens thousands of colonies per day without requiring additional automation. The wide chemical coverage and the high sensitivity of MALDI-MS enable diverse screening projects such as modifying enzymes and functional genomics surveys of gene activation/inhibition libraries.

Choe, Kisurb↗
DOE OSTI2024

Towards using bacterial microcompartments as a platform for spatial metabolic engineering in the industrially important and metabolically versatile Zymomonas mobilis

Advances in synthetic biology have enabled the incorporation of novel biochemical pathways for the production of high-value products into industrially important bacterial hosts. However, attempts to redirect metabolic fluxes towards desired products often lead to the buildup of toxic or undesirable intermediates or, more generally, unwanted metabolic cross-talk. The use of shells derived from self-assembling protein-based prokaryotic organelles, referred to as bacterial microcompartments (BMCs), as a scaffold for metabolic enzymes represents a sophisticated approach that can both insulate and integrate the incorporation of challenging metabolic pathways into industrially important bacterial hosts. Here we took a synthetic biology approach and introduced the model shell system derived from the myxobacterium Haliangium ochraceum (HO shell) into the industrially relevant organism Zymomonas mobilis with the aim of constructing a BMC-based spatial scaffolding platform. SDS-PAGE, transmission electron microscopy, and dynamic light scattering analyses collectively demonstrated the ability to express and purify empty capped and uncapped HO shells from Z. mobilis . As a proof of concept to internally load or externally decorate the shell surface with enzyme cargo, we have successfully targeted fluorophores to the surfaces of the BMC shells. Overall, our results provide the foundation for incorporating enzymes and constructing BMCs with synthetic biochemical pathways for the future production of high-value products in Z. mobilis .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Fossil Corals With Various Degrees of Preservation Can Retain Information About Biomineralization-Related Organic Material

Scleractinian corals typically form a robust calcium carbonate skeleton beneath their living tissue. This skeleton, through its trace element composition and isotope ratios, may record environmental conditions of water surrounding the coral animal. While bulk unrecrystallized aragonite coral skeletons can be used to reconstruct past ocean conditions, corals that have undergone significant diagenesis have altered geochemical signatures and are typically assumed to retain insufficient meaningful information for bulk or macrostructural analysis. However, partially recrystallized skeletons may retain organic molecular components of the skeletal organic matrix (SOM), which is secreted by the animal and directs aspects of the biomineralization process. Some SOM proteins can be retained in fossil corals and can potentially provide past oceanographic, ecological, and indirect genetic information. Here, we describe a dataset of scleractinian coral skeletons, aged from modern to Cretaceous plus a Carboniferous rugosan, characterized for their crystallography, trace element composition, and amino acid compositions. We show that some specimens that are partially recrystallized to calcite yield potentially useful biochemical information whereas complete recrystalization or silicification leads to significant alteration or loss of the SOM fraction. Our analysis is informative to biochemical-paleoceanographers as it suggests that previously discounted partially recrystallized coral skeletons may indeed still be useful at the microstructural level.

58 GEOSCIENCES↗
DOE OSTI2023

Determinants of photochemical characteristics of the photosynthetic electron transport chain of maize

The photosynthetic electron transport chain (ETC) is the bridge that links energy harvesting during the photophysical reactions at one end and energy consumption during the biochemical reactions at the other. Its functioning is thus fundamental for the proper balance between energy supply and demand in photosynthesis. Currently, there is a lack of understanding regarding how the structural properties of the ETC are affected by nutrient availability and plant developmental stages, which is a major roadblock to comprehensive modeling of photosynthesis. Redox parameters reflect the structural controls of ETC on the photochemical reactions and electron transport. We conducted joint measurements of chlorophyll fluorescence (ChlF) and gas exchange under systematically varying environmental conditions and growth stages of maize and sampled foliar nutrient contents. We utilized the recently developed steady-state photochemical model to infer redox parameters of electron transport from these measurements. We found that the inferred values of these photochemical redox parameters varied with leaf macronutrient content. These variations may be caused either directly by these nutrients being components of protein complexes on the ETC or indirectly by their impacts on the structural integrity of the thylakoid and feedback from the biochemical reactions. Also, the redox parameters varied with plant morphology and developmental stage, reflecting seasonal changes in the structural properties of the ETC. Our findings will facilitate the parameterization and simulation of complete models of photosynthesis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Unraveling metabolism underpinning biomass composition shift in Scenedesmus obliquus under simulated outdoor conditions using 13 C-fluxomics

To render the resulting biomass more attractive and amenable for utilization as the basis for low-carbon intensity bioproducts, single-celled algae need to be biochemically and metabolically poised to assimilate and store the delivered carbon in the fastest and most efficient manner. Accelerating biochemical carbon storage, as primarily carbohydrates or lipids, is critical to achieve the high carbon capture potential that is assigned to algae. To guide strain optimization and engineering for maximizing carbon capture and storage, it is essential to elucidate the link between carbon metabolism and biomass composition. Most published metabolomics work in algae remains largely restricted to ideal and simplified environmental conditions in model organisms, thereby limiting their translation to outdoor implementation. In this work, we utilize 13 C isotopic labeling to characterize distinct intracellular metabolic fluxes before, during, and after nitrogen depletion-induced compositional shifts in Scenedesmus obliquus UTEX 393. The results indicate that a transition to carbohydrates is characterized by diverting flux to starch instead of replenishing the Calvin cycle for CO 2 fixation whereas the subsequent transition to lipids is fueled by NADPH produced by upregulating the phosphoenolpyruvate carboxylase (PEPC)–malic enzyme (ME) cycle flux. Our work highlights bottlenecks to carbohydrate- and lipid-rich biomass and can guide implementable strategies to control the fate of fixed carbon in S. obliquus.

09 BIOMASS FUELS↗
DOE OSTI2021

Role of Reactive Oxygen Species and Hormones in Plant Responses to Temperature Changes

Temperature stress is one of the major abiotic stresses that adversely affect agricultural productivity worldwide. Temperatures beyond a plant’s physiological optimum can trigger significant physiological and biochemical perturbations, reducing plant growth and tolerance to stress. Improving a plant’s tolerance to these temperature fluctuations requires a deep understanding of its responses to environmental change. To adapt to temperature fluctuations, plants tailor their acclimatory signal transduction events, and specifically, cellular redox state, that are governed by plant hormones, reactive oxygen species (ROS) regulatory systems, and other molecular components. The role of ROS in plants as important signaling molecules during stress acclimation has recently been established. Here, hormone-triggered ROS produced by NADPH oxidases, feedback regulation, and integrated signaling events during temperature stress activate stress-response pathways and induce acclimation or defense mechanisms. At the other extreme, excess ROS accumulation, following temperature-induced oxidative stress, can have negative consequences on plant growth and stress acclimation. The excessive ROS is regulated by the ROS scavenging system, which subsequently promotes plant tolerance. All these signaling events, including crosstalk between hormones and ROS, modify the plant’s transcriptomic, metabolomic, and biochemical states and promote plant acclimation, tolerance, and survival. Here, we provide a comprehensive review of the ROS, hormones, and their joint role in shaping a plant’s responses to high and low temperatures, and we conclude by outlining hormone/ROS-regulated plant responsive strategies for developing stress-tolerant crops to combat temperature changes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

A Structural Perspective on the RNA Editing of Plant Respiratory Complexes

The last steps of respiration, a core energy-harvesting process, are carried out by a chain of multi-subunit complexes in the inner mitochondrial membrane. Several essential subunits of the respiratory complexes are RNA-edited in plants, frequently leading to changes in the encoded amino acids. While the impact of RNA editing is clear at the sequence and phenotypic levels, the underlying biochemical explanations for these effects have remained obscure. Here, we used the structures of plant respiratory complex I, complex III2 and complex IV to analyze the impact of the amino acid changes of RNA editing in terms of their location and biochemical features. Through specific examples, we demonstrate how the structural information can explain the phenotypes of RNA-editing mutants. This work shows how the structural perspective can bridge the gap between sequence and phenotype and provides a framework for the continued analysis of RNA-editing mutants in plant mitochondria and, by extension, in chloroplasts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

EMD-57033 Augments the Contractility in Porcine Myocardium by Promoting the Activation of Myosin in Thick Filaments

Sufficient cardiac contractility is necessary to ensure the sufficient cardiac output to provide an adequate end-organ perfusion. Inadequate cardiac output and the diminished perfusion of vital organs from depressed myocardium contractility is a hallmark end-stage of heart failure. There are no available therapeutics that directly target contractile proteins to improve the myocardium contractility and reduce mortality. The purpose of this study is to present a proof of concept to aid in the development of muscle activators (myotropes) for augmenting the contractility in clinical heart failure. Here we use a combination of cardiomyocyte mechanics, the biochemical quantification of the ATP turnover, and small angle X-ray diffraction on a permeabilized porcine myocardium to study the mechanisms of EMD-57033 (EMD) for activating myosin. We show that EMD increases the contractility in a porcine myocardium at submaximal and systolic calcium concentrations. Biochemical assays show that EMD decreases the proportion of myosin heads in the energy sparing super-relaxed (SRX) state under relaxing conditions, which are less likely to interact with actin during contraction. Structural assays show that EMD moves the myosin heads in relaxed muscles from a structurally ordered state close to the thick filament backbone, to a disordered state closer to the actin filament, while simultaneously inducing structural changes in the troponin complex on the actin filament. The dual effects of EMD on activating myosin heads and the troponin complex provides a proof of concept for the use of small molecule muscle activators for augmenting the contractility in heart failure.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Using Community Science to Reveal the Global Chemogeography of River Metabolomes

River corridor metabolomes reflect organic matter (OM) processing that drives aquatic biogeochemical cycles. Recent work highlights the power of ultrahigh-resolution mass spectrometry for understanding metabolome composition and river corridor metabolism. However, there have been no studies on the global chemogeography of surface water and sediment metabolomes using ultrahigh-resolution techniques. Here, we describe a community science effort from the Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS) consortium to characterize global metabolomes in surface water and sediment that span multiple stream orders and biomes. We describe the distribution of key aspects of metabolomes including elemental groups, chemical classes, indices, and inferred biochemical transformations. We show that metabolomes significantly differ across surface water and sediment and that surface water metabolomes are more rich and variable. We also use inferred biochemical transformations to identify core metabolic processes shared among surface water and sediment. Finally, we observe significant spatial variation in sediment metabolites between rivers in the eastern and western portions of the contiguous United States. Our work not only provides a basis for understanding global patterns in river corridor biogeochemical cycles but also demonstrates that community science endeavors can enable global research projects that are unfeasible with traditional research models.

54 ENVIRONMENTAL SCIENCES↗