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Results for “Plant biochemistry”

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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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Tight Coupling of Surface and In-Plant Biochemistry and Convection Governs Key Fine Particulate Components over the Amazon Rainforest

We report that throughout the troposphere over the Amazon rainforest, isoprene epoxydiol-secondary organic aerosols (IEPOX-SOA) are key components of submicrometer particle mass. IEPOX-SOA is thought to form by multiphase chemical pathways in the atmosphere, but using detailed model simulations, we show that these pathways are strongly inhibited by the solid particle phase state prevailing in the upper troposphere. We find that 2-methyltetrol gases formed by in-plant biochemical oxidation pathways, their partitioning to fine particles, and dissolution in cloud droplets can explain over 90% of IEPOX-SOA mass concentrations in the upper troposphere. In agreement with previous PM10 chiral measurements, our simulations indicate that plant biochemical processes are the dominant source of particulate 2-methyltetrols in the lower troposphere as well (>70%). Our results imply that in-plant biochemistry plays a central but previously unidentified role in aerosol processes and atmosphere-biosphere-climate interactions over the rainforest.

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

Plant biochemistry influences tropospheric ozone formation, destruction, deposition, and response

Tropospheric ozone (O 3 ) is among the most damaging air pollutant to plants. Plants alter the atmospheric O 3 concentration in two distinct ways: (i) by the emission of volatile organic compounds (VOCs) that are precursors of O 3 ; and (ii) by dry deposition, which includes diffusion of O 3 into vegetation through stomata and destruction by nonstomatal pathways. Isoprene, monoterpenes, and higher terpenoids are emitted by plants in quantities that alter tropospheric O 3 . Deposition of O 3 into vegetation is related to stomatal conductance, leaf structural traits, and the detoxification capacity of the apoplast. The biochemical fate of O 3 once it enters leaves and reacts with aqueous surfaces is largely unknown, but new techniques for the tracking and identification of initial products have the potential to open the black box.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Bacterial Volatile Organic Compounds as a Strategy to Increase Drought Tolerance in Maize (Zea mays L.): Influence on Plant Biochemistry

Maize is highly susceptible to drought, which affects growth and yield. This study investigated how bacterial volatile organic compounds (BVOCs) affect maize drought tolerance. Drought reduced shoot size but increased root length, an adaptation for accessing deeper soil moisture. BVOCs from strain D12 significantly increased root length and shoot growth under drought conditions. Drought also altered root biochemistry, decreasing enzyme activity, and increased osmolyte levels. BVOCs from strains F11 and FS4-14 further increased osmolyte levels but did not protect membranes from oxidative damage, while BVOCs from strains D12 and D7 strains reduced osmolyte levels and cell damage. In shoots, drought increased the levels of osmolytes and oxidative stress markers. BVOCs from FS4-14 had minimal effects on shoot biochemistry. BVOCs from D12 and F11 partially restored metabolic activity but did not reduce cell damage. BVOCs from D7 reduced metabolic activity and cell damage. These results suggest that BVOCs can modulate the biochemical response of maize to drought, with some strains evidencing the potential to enhance drought tolerance.

Lopes, Tiago (ORCID:0000000330603315)↗
DOE OSTI2025

Metal concentration and leaf spatial distribution assessed by synchrotron µXRF in Brazilian nickel hyperaccumulators

Background and Aims: The limited number of known hyperaccumulator species in tropical regions, including Brazil, has hampered the development of nickel (Ni) agromining. In addition, the mechanisms underlying metal accumulation and distribution in these species remain poorly understood, despite their pivotal role in identifying species with economic potential. Furthermore, this study assessed the accumulation potential and foliar spatial distribution of metals in three Brazilian hyperaccumulator species (Pfaffia sarcophylla, Justicia lanstyakii, and Lippia lupulina) growing in one of the world’s largest mafic–ultramafic complexes. Methods Concentrations of Ni and other metals in leaves were determined using portable X-ray fluorescence (pXRF) and inductively coupled plasma optical emission spectroscopy (ICP-OES). Synchrotron-based X-ray microfluorescence (SR-µXRF) was employed to map the spatial distribution of metals across intact leaves. Results: The results revealed leaf Ni concentrations ranging from 320 to 1,950 mg kg⁻ 1 in P. sarcophylla, 1,640 to 6,810 mg kg⁻ 1 in L. lupulina, and 1,990 to 4,900 mg kg⁻ 1 in J. lanstyakii. Nickel, Mn, and Co exhibited similar distribution patterns, concentrating mainly in the leaf margins and veins across all species, while Ca, K, and Mg co-localization suggests regulatory mechanisms for adaptation. Conclusion: Although these plants exhibited Ni hyperaccumulation, our findings suggest limited commercial potential for agromining. Further research on genetic variability and nutrient assimilation, particularly in P. sarcophylla, is recommended to elucidate the mechanisms underlying Ni accumulation and intraspecific variability.

36 MATERIALS SCIENCE↗
DOE OSTI2024

The crystal structure of Grindelia robusta 7,13-copalyl diphosphate synthase reveals active site features controlling catalytic specificity

Diterpenoid natural products serve critical functions in plant development and ecological adaptation and many diterpenoids have economic value as bioproducts. The family of class II diterpene synthases catalyzes the committed reactions in diterpenoid biosynthesis, converting a common geranylgeranyl diphosphate precursor into different bicyclic prenyl diphosphate scaffolds. Enzymatic rearrangement and modification of these precursors generate the diversity of bioactive diterpenoids. We report the crystal structure of Grindelia robusta 7,13-copalyl diphosphate synthase, GrTPS2, at 2.1 Å of resolution. GrTPS2 catalyzes the committed reaction in the biosynthesis of grindelic acid, which represents the signature metabolite in species of gumweed (Grindelia spp., Asteraceae). Grindelic acid has been explored as a potential source for drug leads and biofuel production. The GrTPS2 crystal structure adopts the conserved three-domain fold of class II diterpene synthases featuring a functional active site in the γβ-domain and a vestigial α-domain. Substrate docking into the active site of the GrTPS2 apo protein structure predicted catalytic amino acids. Biochemical characterization of protein variants identified residues with impact on enzyme activity and catalytic specificity. Specifically, mutagenesis of Y457 provided mechanistic insight into the position-specific deprotonation of the intermediary carbocation to form the characteristic 7,13 double bond of 7,13-copalyl diphosphate.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Biomass Demineralization: A Critical Need for Future Biorefineries

Biomass contains up to 14 essential elements that serve as nutrients for plant growth and development, including photosynthesis and enzyme functionalities. These elements in different chemical forms (e.g., minerals) constitute the inorganic fraction of biomass and can cause operational issues in thermal and biochemical biomass conversion technologies. In biomass gasification and pyrolysis processes, for instance, inorganics can cause fouling, tar formation, and corrosion. In catalytic and biochemical processes, inorganics can poison catalysts, alter biochemical pathways, and modify product yields and selectivity. This review provides an overview of the inorganic content in biomass feedstocks, the critical role inorganics play in plant biochemistry, the effect that inorganics have in various thermochemical and biochemical biomass conversion technologies, and different approaches to remove them from biomass. We provide recommendations for future research, focusing on developing technologies to effectively remove inorganics from biomass, using the inorganics to improve soil quality and for alternative applications, and designing biorefineries to convert demineralized biomass obtained from diverse sources.

09 - BIOMASS FUELS↗
DOE OSTI2023

Harnessing Plant Sugar Metabolism for Glycoengineering

Plants possess an innate ability to generate vast amounts of sugar and produce a range of sugar-derived compounds that can be utilized for applications in industry, health, and agriculture. Nucleotide sugars lie at the unique intersection of primary and specialized metabolism, enabling the biosynthesis of numerous molecules ranging from small glycosides to complex polysaccharides. Plants are tolerant to perturbations to their balance of nucleotide sugars, allowing for the overproduction of endogenous nucleotide sugars to push flux towards a particular product without necessitating the re-engineering of upstream pathways. Pathways to produce even non-native nucleotide sugars may be introduced to synthesize entirely novel products. Heterologously expressed glycosyltransferases capable of unique sugar chemistries can further widen the synthetic repertoire of a plant, and transporters can increase the amount of nucleotide sugars available to glycosyltransferases. In this opinion piece, we examine recent successes and potential future uses of engineered nucleotide sugar biosynthetic, transport, and utilization pathways to improve the production of target compounds. Additionally, we highlight current efforts to engineer glycosyltransferases. Ultimately, the robust nature of plant sugar biochemistry renders plants a powerful chassis for the production of target glycoconjugates and glycans.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

The Global Spectra-Trait Initiative: A database of paired leaf spectroscopy and functional traits associated with leaf photosynthetic capacity (v1.0.0)

The Global Spectra-Trait Initiative (GSTI) aims to generate generalizable spectra trait models using reflectance data to predict leaf traits associated with the photosynthesis capacity of leaves. It comprises a synthesized dataset of leaf trait data, input datasets and code. Leaf traits include the maximum carboxylation rate of rubisco (Vcmax), the maximum electron transport rate (Jmax), the dark respiration, as well as the prediction of leaf nitrogen, leaf mass per area (LMA), and leaf water content (LWC). The dataset comprises >7500 paired observations from around 400 species from a broad range of biomes. This dataset comprises a zip file of the GSTI GitHub repository (https://github.com/plantphys/gsti), the synthesized database (.csv) and database metadata files. This dataset was updated on 2025-12-12 with minor edits to mirror the accepted manuscript version and GitHub release (Version 1.0.0 (ESSD accepted version)). Edits included minor changes to the project documentation on GitHub and removal of 12 duplicate entries from the database.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Imaging plant metabolism in situ

Abstract Mass spectrometry imaging (MSI) has emerged as an invaluable analytical technique for investigating the spatial distribution of molecules within biological systems. In the realm of plant science, MSI is increasingly employed to explore metabolic processes across a wide array of plant tissues, including those in leaves, fruits, stems, roots, and seeds, spanning various plant systems such as model species, staple and energy crops, and medicinal plants. By generating spatial maps of metabolites, MSI has elucidated the distribution patterns of diverse metabolites and phytochemicals, encompassing lipids, carbohydrates, amino acids, organic acids, phenolics, terpenes, alkaloids, vitamins, pigments, and others, thereby providing insights into their metabolic pathways and functional roles. In this review, we present recent MSI studies that demonstrate the advances made in visualizing the plant spatial metabolome. Moreover, we emphasize the technical progress that enhances the identification and interpretation of spatial metabolite maps. Within a mere decade since the inception of plant MSI studies, this robust technology is poised to continue as a vital tool for tackling complex challenges in plant metabolism.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2025

Molecular level insight into non-bilayer structure formation in thylakoid membranes: a molecular dynamics study

In oxygenic photosynthetic organisms, the light reactions are performed by protein complexes embedded in the lipid bilayer of thylakoid membranes (TMs). The organization of the bulk lipid molecules into bilayer structures provide optimal conditions for the build-up of the proton motive force (pmf) and its utilization for ATP synthesis. However, the lipid composition of TMs is dominated by the non-bilayer lipid species monogalactosyl diacylglycerol (MGDG), and functional plant TMs, besides the bilayer, contain large amounts of non-bilayer lipid phases. Bulk lipids have been shown to be associated with lumenal, stromal-side and marginal-region proteins and proposed to play roles in the self-assembly and photoprotection of the photosynthetic machinery. Furthermore, it has recently been pointed out that the generation and utilization of pmf for ATP synthesis according to the ‘protet’ or protonic charge transfer model Kell (Biochim Biophys Acta Bioenerg 1865(4):149504, 2024), requires high MGDG content Garab (Physiol Plant 177(2):e70230, 2025). In this study, to gain better insight into the structural and functional roles of MGDG, we employed all atom and coarse-grained molecular dynamics simulations to explore how temperature, hydration levels and varying MGDG concentrations affect the structural and dynamic properties of bilayer membranes constituted of plant thylakoid lipids. Our findings reveal that MGDG promotes increased membrane fluidity and dynamic fluctuations in membrane thickness. MGDG-rich stacked bilayers spontaneously formed inverted hexagonal phases; these transitions were enhanced at low hydration levels and at elevated but physiologically relevant temperatures. It can thus be inferred that MGDG plays important roles in heat and drought stress mechanisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

A structural explanation for the mechanism and specificity of plant branching enzymes I and IIb

Branching enzymes (BEs) are essential in the biosynthesis of starch and glycogen and play critical roles in determining the fine structure of these polymers. The substrates of these BEs are long carbohydrate chains that interact with these enzymes via multiple binding sites on the enzyme’s surface. By controlling the branched-chain length distribution, BEs can mediate the physiological properties of starch and glycogen moieties; however, the mechanism and structural determinants of this specificity remain mysterious. In this study, we identify a large dodecaose binding surface on rice BE I (BEI) that reaches from the outside of the active site to the active site of the enzyme. Mutagenesis activity assays confirm the importance of this binding site in enzyme catalysis, from which we conclude that it is likely the acceptor chain binding site. Comparison of the structures of BE from Cyanothece and BE1 from rice allowed us to model the location of the donor-binding site. We also identified two loops that likely interact with the donor chain and whose sequences diverge between plant BE1, which tends to transfer longer chains, and BEIIb, which transfers exclusively much shorter chains. When the sequences of these loops were swapped with the BEIIb sequence, rice BE1 also became a short-chain transferring enzyme, demonstrating the key role these loops play in specificity. Taken together, these results provide a more complete picture of the structure, selectivity, and activity of BEs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

mzPeak: Designing a Scalable, Interoperable, and Future-Ready Mass Spectrometry Data Format

Advances in mass spectrometry (MS) instrumentation, such as higher resolution, faster scan speeds, and improved sensitivity, have significantly increased the volume and complexity of data. The growing adoption of imaging and ion mobility further amplifies these challenges across MS-based omics fields, including proteomics, metabolomics, and lipidomics. While these technologies unlock new possibilities, they also present significant challenges in data management, storage, and accessibility. Existing open formats, such as the XML-based community standards mzML and imzML, struggle to meet the demands of modern MS workflows due to their large file sizes, slow data access, and limited metadata support. Vendor-specific formats, while optimized for proprietary instruments, lack interoperability, comprehensive metadata support and long-term archival reliability. This white paper lays the groundwork for mzPeak, a next-generation community data format designed to address these challenges and support high-throughput, multi-dimensional MS workflows. By adopting a hybrid model that combines efficient binary storage for numerical data and both human and machine-readable metadata storage, mzPeak will reduce file sizes, accelerate data access, and offer a scalable, adaptable solution for evolving MS technologies. For researchers, mzPeak will enable enhanced interoperability across platforms, seamless support for complex workflows including ion mobility and MS imaging, and faster data access compared to existing community formats such as mzML. Its design will ensure data is managed in compliance with regulatory standards, essential for applications such as precision medicine and chemical safety, where long-term data integrity and accessibility are critical. For vendors, mzPeak provides a streamlined, open alternative to proprietary formats, reducing the burden of regulatory compliance while aligning with the industry's push for transparency and standardization. By offering a high-performance, interoperable solution, mzPeak positions vendors to meet customer demands for sustainable data management tools which will be able to handle emerging and future data types and workflows. mzPeak aspires to become the cornerstone of MS data management, empowering researchers, vendors, and developers to innovate and collaborate more effectively.

data formats↗
DOE OSTI2022

Transgenic manipulation of triacylglycerol biosynthetic enzymes in B. napus alters lipid-associated gene expression and lipid metabolism

Abstract Oilseed rape ( Brassica napus ) is an important crop that is cultivated for the oil (mainly triacylglycerol; TAG) it produces in its seeds. TAG synthesis is controlled mainly by key enzymes in the Kennedy pathway, such as glycerol 3-phosphate acyltransferase (GPAT), lysophosphatidate acyltransferase (LPAT) and diacylglycerol acyltransferase (DGAT) but can also be produced from phosphoglycerides such as phosphatidylcholine (PC) by the activity of the enzyme phospholipid: diacylglycerol acyltransferase (PDAT). To evaluate the potential for these enzymes to alter oil yields or composition, we analysed transgenic B. napus lines which overexpressed GPAT, LPAT or PDAT using heterologous transgenes from Arabidopsis and Nasturtium and examined lipid profiles and changes in gene expression in these lines compared to WT. Distinct changes in PC and TAG abundance and spatial distribution in embryonic tissues were observed in some of the transgenic lines, together with altered expression of genes involved generally in acyl-lipid metabolism. Overall our results show that up-regulation of these key enzymes differentially affects lipid composition and distribution as well as lipid-associated gene expression, providing important information which could be used to improve crop properties by metabolic engineering.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Structure and function of a flavin-dependent S-monooxygenase from garlic ( Allium sativum )

Allicin is a component of the characteristic smell and flavor of garlic ( Allium sativum ). A flavin-containing monooxygenase (FMO) produced by A. sativum (AsFMO) was previously proposed to oxidize S-allyl- L -cysteine (SAC) to alliin, an allicin precursor. In this paper, we present a kinetic and structural characterization of AsFMO that suggests a possible contradiction to this proposal. Results of steady-state kinetic analyses revealed that AsFMO exhibited negligible activity with SAC; however, the enzyme was highly active with L -cysteine, N-acetyl- L -cysteine, and allyl mercaptan. We found that allyl mercaptan with NADPH was the preferred substrate-cofactor combination. Rapid-reaction kinetic analyses showed that NADPH binds tightly ($K_D$ of ~2 μM) to AsFMO and that the hydride transfer occurs with pro-R stereospecificity. We detected the formation of a long-wavelength band when AsFMO was reduced by NADPH, probably representing the formation of a charge-transfer complex. In the absence of substrate, the reduced enzyme, in complex with NADP + , reacted with oxygen and formed an intermediate with a spectrum characteristic of C4a-hydroperoxyflavin, which decays several orders of magnitude more slowly than the $k$ cat . The presence of substrate enhanced C4a-hydroperoxyflavin formation and, upon hydroxylation, oxidation occurred with a rate constant similar to the $k$ cat . The structure of AsFMO complexed with FAD at 2.08-Å resolution features two domains for binding of FAD and NADPH, representative of class B flavin monooxygenases. These biochemical and structural results are consistent with AsFMO being an S-monooxygenase involved in allicin biosynthesis through direct formation of sulfenic acid and not SAC oxidation.

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

Proteins associated with the Arabidopsis thaliana plastid rhomboid-like protein RBL10

Rhomboid-like proteins are intramembrane proteases with a variety of regulatory roles in cells. Though many rhomboid-like proteins are predicted in plants, their detailed molecular mechanisms or cellular functions are not yet known. Of the 13 predicted rhomboids in Arabidopsis thaliana, one, RBL10, affects lipid metabolism in the chloroplast, because in the respective rbl10 mutant the transfer of phosphatidic acid through the inner envelope membrane is disrupted. Here we show that RBL10 is part of a high-molecular-weight complex of 250 kDa or greater in size. Nine likely components of this complex are identified by two independent methods and include Acyl Carrier Protein 4 (ACP4) and Carboxyltransferase Interactor1 (CTI1), which have known roles in chloroplast lipid metabolism. The acp4 mutant has decreased C16:3 fatty acid content of monogalactosyldiacylglycerol, similar to the rbl10 mutant, prompting us to offer a mechanistic model of how an interaction between ACP4 and RBL10 might affect chloroplast lipid assembly. We also demonstrate the presence of a seventh transmembrane domain in RBL10, refining the currently accepted topology of this protein. Taken together, the identity of possible RBL10 complex components as well as insights into RBL10 topology and distribution in the membrane provide a stepping-stone towards a deeper understanding of RBL10 function in Arabidopsis lipid metabolism.

59 BASIC BIOLOGICAL SCIENCES↗