Search NASA⌕ Search

SEARCH · Search NASA

Results for “biological redox”

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 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

The physiological basis for estimating photosynthesis from Chl>em>a fluorescence

We report solar-induced Chl fluorescence (SIF) offers the potential to curb large uncertainties in the estimation of photosynthesis across biomes and climates, and at different spatiotemporal scales. However, it remains unclear how SIF should be used to mechanistically estimate photosynthesis. In this study, we built a quantitative framework for the estimation of photosynthesis, based on a mechanistic light reaction model with the Chla fluorescence of Photosystem II (SIFPSII) as an input (MLR-SIF). Utilizing 29 C 3 and C 4 plant species that are representative of major plant biomes across the globe, we confirmed the validity of this framework at the leaf level. The MLR-SIF model is capable of accurately reproducing photosynthesis for all C 3 and C 4 species under diverse light, temperature, and CO 2 conditions. We further tested the robustness of the MLR-SIF model using Monte Carlo simulations, and found that photosynthesis estimates were much less sensitive to parameter uncertainties relative to the conventional Farquhar, von Caemmerer, Berry (FvCB) model because of the additional independent information contained in SIF PSII . Once inferred from direct observables of SIF, SIF PSII provides ‘parameter savings’ to the MLR-SIF model, compared to the mechanistically equivalent FvCB model, and thus avoids the uncertainties arising as a result of imperfect model parameterization. Our findings set the stage for future efforts to employ SIF mechanistically to improve photosynthesis estimates across a variety of scales, functional groups, and environmental conditions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Biogeochemical Processes Across Aquatic Interfaces

The aquatic interfaces exposing terrestrial soils to oxic-anoxic regime shifts represent biogeochemical “hotspots” that are extremely sensitive to climate and environmental change. However, processes and interaction across theses aquatic interfaces are poorly understood and underrepresented in current Earth system models. In this project, we aim to develop predictive understanding of the feedbacks between microbial systems and geochemical environments that determine emergent ecosystem behaviors and resilience in response to disturbances. We use experimental, mechanistic modeling and meta-analysis tools to elucidate interactions among soil, water, geomorphology and microbiology that regulate the molecular transformations and fluxes of carbon, nutrients, and redox-sensitive compounds across aquatic interfaces.

58 GEOSCIENCES↗
DOE OSTI2020

Utilization of protein film electrochemistry to characterize the mechanisms imparting aerotolerance and bidirectionality in soluble, multimeric [NiFe]-hydrogenases (Final Report for Grant No. DE-SC0008074)

The overall goal of this project was to better understand how structural features control functional aspects of enzymes involved in catalysis in which a substrate is oxidized or reduced. Two types of model enzymes were explored: the soluble [NiFe]-hydrogenase from Pyrococcus furiousus and the thiosulfate reductase from Pyrobaculum aerophilum. Both are models for complex, multielectron transformations such as nitrogen and carbon dioxide reduction, and parts of important biogeochemical cycles. In this project, electrochemical methods were used to define the activities of these enzymes and targeted variants designed to modulate activity. We showed that the catalytic activity of the soluble hydrogenase from Pyrococcus furiosus can be modulated by removing large parts of the enzyme far from the active site. This surprising result suggests that interactions between functional centers far apart within the enzyme may be essential for controlling and tuning activity. We also showed that the catalytic activity of thiosulfate reductase from Pyrobaculum aerophilum can be modulated by changing the metal at the active site to be either molybdenum or tungsten. These results contribute to our understanding of how the protein environment can tune the reactivity of an embedded metal, catalytic center. The results were and are being published in peer-reviewed, scientific publications.

08 HYDROGEN↗
DOE OSTI2020

Redox and Thiols in Archaea

Low molecular weight (LMW) thiols have many functions in bacteria and eukarya, ranging from redox homeostasis to acting as cofactors in numerous reactions, including detoxification of xenobiotic compounds. The LMW thiol, glutathione (GSH), is found in eukaryotes and many species of bacteria. Analogues of GSH include the structurally different LMW thiols: bacillithiol, mycothiol, ergothioneine, and coenzyme A. Many advances have been made in understanding the diverse and multiple functions of GSH and GSH analogues in bacteria but much less is known about distribution and functions of GSH and its analogues in archaea, which constitute the third domain of life, occupying many niches, including those in extreme environments. Archaea are able to use many energy sources and have many unique metabolic reactions and as a result are major contributors to geochemical cycles. As LMW thiols are major players in cells, this review explores the distribution of thiols and their biochemistry in archaea.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Redox Biochemistry of Energy Conservation in Methanogens and their Syntrophic Partners

The primary objective of this project was to uncover previously unknown modes by which living organisms harvested energy. Specifically, it queried microbial systems, which were once thought to not be able to utilize oxygen. Through the use of cutting-edge approaches, we were able to identify novel mechanistic processes that allow organisms to thrive under varying environmental conditions. This constitutes a paradigm shift in the field. Our work has opened new vistas for expanding the horizons of energy conservation in biological systems, as well as shed light on green energy innovations.

59 BASIC BIOLOGICAL SCIENCES↗
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 OSTI2024

PPI DataHub Project Data Package: S. elongatus PCC 7942 Circadian Control Bioproduction Transcriptomics (PB-DP3)

The purpose of this experiment was to evaluate how circadian clock regulation impacts carbon partitioning between storage, growth, and product synthesis in Synechococcus elongatus PCC 7942 in providing insights to strategies for enhanced bioproduction. Sample data was acquired using a Illumina HiSeq sequencer system and processed for RNA sequencing (RNA-Seq) expression analysis. Transcriptomic differential expression analysis revealed coordinated circadian clock-driven adjustment of the cell cycle and rewiring of energy and carbon metabolism. Processed RNA-Seq datasets are openly accessible from the PNNL DataHub project dataset download page and contain secondary processed RNA-seq results files and supporting metadata materials linked to relevant source code information supporting data transparency and reuse.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Molecular mechanism of Rubisco activase: Dynamic assembly and Rubisco remodeling

Ribulose-1,5-bisphosphate (RuBP) carboxylase-oxygenase (Rubisco) enzyme is the limiting step of photosynthetic carbon fixation, and its activation is regulated by its co-evolved chaperone, Rubisco activase (Rca). Rca removes the intrinsic sugar phosphate inhibitors occupying the Rubisco active site, allowing RuBP to split into two 3-phosphoglycerate (3PGA) molecules. This review summarizes the evolution, structure, and function of Rca and describes the recent findings regarding the mechanistic model of Rubisco activation by Rca. New knowledge in these areas can significantly enhance crop engineering techniques used to improve crop productivity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Scrambling Signal Modularity in Bottom-up Assembled Synthetic Pseudomonas Consortia Reveals Robust Information Transfer

There is immense potential in crafting synthetic microbial communities for application in human health, agriculture, the environment, and even biomanufacturing where an appropriately constructed consortium can be assembled with tremendous biosynthetic or degradative capabilities. In many of these cases, bacterial signaling serves as a form of intercellular information transfer that guides the collective’s behavior. Such communication is complex, as many signals, signal disruptors, microbial species, physical barriers, and spatiotemporal constraints may be involved. Here, in this work, we demonstrate that a multisignal pathway for molecular information transfer within a consortium of several Pseudomonas spp. can be scrambled (genetically and organizationally) while the original message is still effectively conveyed. Assembled from the bottom up, we have employed two types of signaling molecules (i) a redox active secondary metabolite (rhizospheric signal, phloroglucinol), and (ii) a bacterial quorum sensing signal (3-oxo-C12 acylhomoserine lactone, AI-1). These signals can be intraconverted and acted upon by designated community members. We show how the order in which the signals are received, transduced, and subsequently transmitted can be rearranged with minimal impact on the intended outcome. In the consortial context, we found this messaging structure can be remarkably robust. Inspired by rhizospheric molecular signaling mechanisms, this work provides a conceptual framework for designing signaling and information transfer processes within assembled communities.

Biological and medical sciences↗
DOE OSTI2026

Comparative Dissolution of Iron-Bearing Minerals by Catecholate and Hydroxamate Siderophores under Oxic and Anoxic Conditions

Siderophores play a crucial role in biological iron (Fe) acquisition and mobilization by promoting Fe mineral and rock weathering. While the effects of the hydroxamate siderophore desferrioxamine B (DFOB) have been extensively studied, the role of catecholates in the dissolution of Fe mineral and rock under varying redox conditions remain limited. Moreover, despite Fe being one of the most redox-active metals, the siderophore-mediated redox transformations of solid-phase Fe and their impact on mineral dissolution are not well understood. Herein, this study systematically investigated dissolution behavior of both Fe(II) and Fe(III)-bearing minerals and rocks (Fe(II)- bearing basalt and olivine, and Fe(III)- bearing nontronite and goethite), by two structurally distinct biological siderophores, catecholate protochelin and hydroxamate DFOB, under both oxic and anoxic conditions. Batch experiments quantified Fe and transition metals (Mn, Ni, Zn, Mo) released from the tested minerals in the presence of siderophores. Throughout the dissolution experiments, siderophore concentrations and Fe-siderophore complexation in solutions were measured using UV-vis spectrometry. Fe redox changes under oxic and anoxic conditions by siderophores were determined, and mineral surface alterations following siderophore treatments were characterized through scanning electron microscopy (SEM) and time-of-flight secondary ion mass spectroscopy (ToF-SIMS). Results revealed distinct interplays of dissolution mechanisms, including ligand-exchange promoted dissolution and reductive dissolution, along with Fe(III) reduction and Fe(II) oxidation, contributing to the Fe(II)- and Fe(III)-rich mineral weathering under varying redox conditions. Under oxic conditions, both protochelin and DFOB enhanced Fe release from Fe(II)-rich basalt and olivine more effectively than from Fe(III)-rich minerals. DFOB induced greater Fe(II)-mineral dissolution than protochelin. This difference was attributed to a higher level of Fe(II) oxidation by DFOB in contrast to protochelin, as well as the protochelin oxidation with the loss of Fe binding groups (catechols). Under anoxic conditions, both siderophores significantly reduced Fe(III) in nontronite and goethite, with protochelin demonstrating substantially stronger Fe(III) reduction capacity than DFOB. However, Fe(III) reduction negatively impacted Fe release from Fe(III)-rich minerals. Instead, Fe release from Fe(II)-rich minerals was enhanced under anoxic conditions due to the absence of Fe(II) oxidation and labile Fe(II). Variations in siderophore adsorption also contributed to dissolution differences. Beyond iron, the release of transition metals from tested minerals was influenced by elemental contents, mineral compositions, and siderophore types, revealing distinct metal- and siderophore-dependent patterns. This systematic investigation highlights the roles of siderophores in Fe redox cycling and metal mobilization, enhancing our understanding of different siderophore behaviors in siderophore-mediated microbial metal acquisition within redox-dynamic environments, with implications for bioleaching industries and applications in agriculture and climate change mitigation.

Guo, Dongyi↗
DOE OSTI2024

Signatures of cysteine oxidation on muscle structural and contractile proteins are associated with physical performance and muscle function in older adults: Study of Muscle, Mobility and Aging (SOMMA)

Oxidative stress is considered a contributor to declining muscle function and mobility during aging; however, the underlying molecular mechanisms remain poorly described. We hypothesized that greater levels of cysteine (Cys) oxidation on muscle proteins are associated with decreased measures of mobility. Herein, we applied a novel redox proteomics approach to measure reversible protein Cys oxidation in vastus lateralis muscle biopsies collected from 56 subjects in the Study of Muscle, Mobility and Aging (SOMMA), a community-based cohort study of individuals aged 70 years and older. We tested whether levels of Cys oxidation on key muscle proteins involved in muscle structure and contraction were associated with muscle function (leg power and strength), walking speed, and fitness (VO 2 peak on cardiopulmonary exercise testing) using linear regression models adjusted for age, sex, and body weight. Higher oxidation levels of select nebulin Cys sites were associated with lower VO 2 peak, while greater oxidation of myomesin-1, myomesin-2, and nebulin Cys sites was associated with slower walking speed. Higher oxidation of Cys sites in key proteins such as myomesin-2, alpha-actinin-2, and skeletal muscle alpha-actin were associated with lower leg power and strength. We also observed an unexpected correlation (R = 0.48) between a higher oxidation level of eight Cys sites in alpha-actinin-3 and stronger leg power. Despite this observation, the results generally support the hypothesis that Cys oxidation of muscle proteins impairs muscle power and strength, walking speed, and cardiopulmonary fitness with aging.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Hydrogen–Deuterium Exchange Mass Spectrometry Identifies Local and Long-Distance Interactions within the Multicomponent Radical SAM Enzyme, PqqE

Interactions among proteins and peptides are essential for many biological activities including the tailoring of peptide substrates to produce natural products. The first step in the production of the bacterial redox cofactor pyrroloquinoline quinone (PQQ) from its peptide precursor is catalyzed by a radical SAM (rSAM) enzyme, PqqE. We describe the use of hydrogen–deuterium exchange mass spectrometry (HDX-MS) to characterize the structure and conformational dynamics in the protein–protein and protein–peptide complexes necessary for PqqE function. HDX-MS-identified hotspots can be discerned in binary and ternary complex structures composed of the peptide PqqA, the peptide-binding chaperone PqqD, and PqqE. Structural conclusions are supported by size-exclusion chromatography coupled to small-angle X-ray scattering (SEC-SAXS). HDX-MS further identifies reciprocal changes upon the binding of substrate peptide and S-adenosylmethionine (SAM) to the PqqE/PqqD complex: long-range conformational alterations have been detected upon the formation of a quaternary complex composed of PqqA/PqqD/PqqE and SAM, spanning nearly 40 Å, from the PqqA binding site in PqqD to the PqqE active site Fe 4 S 4 . Interactions among the various regions are concluded to arise from both direct contact and distal communication. The described experimental approach can be readily applied to the investigation of protein conformational communication among a large family of peptide-modifying rSAM enzymes.

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

PPI DataHub Project Data Package: S. elongatus PCC 7942 Limited Proteolysis and Thermal Proteome Profiling Structural Proteomics (JM-PB-DP3)

The purpose of this experiment was to investigate structural alterations in proteins involved in central carbon metabolism and photosynthetic electron transfer pathways in Synechococcus elongatus PCC 7942. Sample data was obtained from S. elongatus cell lysates using three complementary mass spectrometry (MS) techniques using limited proteolysis (LiP-MS), thermal proteome profiling (TPP-MS), and redox enrichment (Redox-MS) in evaluating alterations solvent accessibility and structural stability caused by light perturbation at the molecular level. Experimentally processed sample data for LiP and TPP proteomic datasets were derived from the same cell culture stock, prepared simultaneously in parallel, and acquired by mass spectrometry. Processed datasets are openly accessible from the download button and contain secondary processed proteomic results files, computed outputs, and supporting metadata materials. Experimental samples processed for LiP-MS label-free quantification (LFQ) or TPP-MS tandem mass tag (TMT) 10-plex were acquired using a Q-Exactive HF-X mass spectrometer and processed/compiled using either MSGF+ (v2024.03.26) or ​​​​PlexedPiper for proteome evaluation. Additional software supporting downstream proteomic analysis include FragPipe (v.4.0), MSFragger (v.22.1), and an adapted Microbial Isolate LiP Analysis Workflow (located at Zenodo). Processed proteomic data downloads include a sample naming key, normalized quantification results files, and processed protein annotated abundance files.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Redox Poise during Rhodospirillum rubrum Phototrophic Growth Drives Large-scale Changes in Macromolecular Synthesis Pathways

During photoheterotrophic growth on organic substrates, purple nonsulfur photosynthetic bacteria like Rhodospirillum rubrum can acquire electrons by multiple means, including oxidation of organic substrates, oxidation of inorganic electron donors (e.g., H2), and by reverse electron flow from the photosynthetic electron transport chain. These electrons are stored as reduced electron-carrying cofactors (e.g., NAD(P)H and ferredoxin). The overall ratio of oxidized to reduced cofactors (e.g., NAD(P)+:NAD(P)H), or ’redox poise’, is difficult to understand or predict, as are the cellular processes for dissipating these reducing equivalents. Using physics-based models that capture mass action kinetics consistent with the thermodynamics of reactions and pathways, a range of redox conditions for heterophototrophic growth are evaluated, from conditions in which the NADP+/NADPH levels approach thermodynamic equilibrium to conditions in which the NADP+/NADPH ratio is far above the typical physiological values. Modeling predictions together with experimental measurements indicate that the redox poise of the cell results in large-scale changes in the activity of biosynthetic pathways and, thus, changes in cell macromolecule levels (DNA, RNA, proteins, and fatty acids). Furthermore, modeling predictions indicate that during phototrophic growth, reverse electron flow from the quinone pool is a minor contributor to the production of reduced cofactors (e.g., NAD(P)H) compared to other oxidative processes (H2 and carbon substrate oxidation). Instead, the quinone pool primarily operates to aid ATP production. The high level of ATP, in turn, drives reduction processes even when NADPH levels are relatively low compared to NADP+ by coupling ATP hydrolysis to the reductive processes. The model, in agreement with experimental measurements of macromolecule ratios of cells growing on different carbon substrates, indicates that the dynamics of nucleotide versus lipid and protein production is likely a significant mechanism of balancing oxidation and reduction in the cell.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Catalase protects against nonenzymatic decarboxylations during photorespiration in Arabidopsis thaliana

Abstract Photorespiration recovers carbon that would be otherwise lost following the oxygenation reaction of rubisco and production of glycolate. Photorespiration is essential in plants and recycles glycolate into usable metabolic products through reactions spanning the chloroplast, mitochondrion, and peroxisome. Catalase in peroxisomes plays an important role in this process by disproportionating H 2 O 2 resulting from glycolate oxidation into O 2 and water. We hypothesize that catalase in the peroxisome also protects against nonenzymatic decarboxylations between hydrogen peroxide and photorespiratory intermediates (glyoxylate and/or hydroxypyruvate). We test this hypothesis by detailed gas exchange and biochemical analysis of Arabidopsis thaliana mutants lacking peroxisomal catalase. Our results strongly support this hypothesis, with catalase mutants showing gas exchange evidence for an increased stoichiometry of CO 2 release from photorespiration, specifically an increase in the CO 2 compensation point, a photorespiratory‐dependent decrease in the quantum efficiency of CO 2 assimilation, increase in the 12 CO 2 released in a 13 CO 2 background, and an increase in the postillumination CO 2 burst. Further metabolic evidence suggests this excess CO 2 release occurred via the nonenzymatic decarboxylation of hydroxypyruvate. Specifically, the catalase mutant showed an accumulation of photorespiratory intermediates during a transient increase in rubisco oxygenation consistent with this hypothesis. Additionally, end products of alternative hypotheses explaining this excess release were similar between wild type and catalase mutants. Furthermore, the calculated rate of hydroxypyruvate decarboxylation in catalase mutant is much higher than that of glyoxylate decarboxylation. This work provides evidence that these nonenzymatic decarboxylation reactions, predominately hydroxypyruvate decarboxylation, can occur in vivo when photorespiratory metabolism is genetically disrupted.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Domain crossover in the reductase subunit of NADPH-dependent assimilatory sulfite reductase

NADPH-dependent assimilatory sulfite reductase (SiR) from Escherichia coli performs a six-electron reduction of sulfite to the bioavailable sulfide. SiR is composed of a flavoprotein (SiRFP) reductase subunit and a hemoprotein (SiRHP) oxidase subunit. There is no known high-resolution structure of SiR or SiRFP, thus we do not yet fully understand how the subunits interact to perform their chemistry. Here, we used small-angle neutron scattering to understand the impact of conformationally restricting the highly mobile SiRFP octamer into an electron accepting (closed) or electron donating (open) conformation, showing that SiR remains active, flexible, and asymmetric even with these conformational restrictions. From these scattering data, we then model the first solution structure of SiRFP. Further, computational modeling of the N-terminal 52 amino acids that are responsible for SiRFP oligomerization suggests an eight-helical bundle tethers together the SiRFP subunits to form the SiR core. Finally, mass spectrometry analysis of the closed SiRFP variant show that SiRFP is capable of inter-molecular domain crossover, in which the electron donating domain from one polypeptide is able to interact directly with the electron accepting domain of another polypeptide. This structural characterization suggests that SiR performs its high-volume electron transfer through both inter- and intramolecular pathways between SiRFP domains and, thus, cis or trans transfer from reductase to oxidase subunits. Such highly redundant potential for electron transfer makes this system a potential target for designing synthetic enzymes.

59 BASIC BIOLOGICAL SCIENCES↗