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Results for “Oxidoreductases”

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 OSTI2026

Catabolism of lignin-related methoxylated compounds in white-rot fungi utilizes non-canonical oxidoreductases

White-rot fungi (WRF) are the most effective lignin-degrading organisms in nature, making them essential to Earth’s carbon cycle. Lignin is a highly methoxylated, heterogeneous biopolymer derived from plants. However, the pathways WRF use to metabolize methoxylated aromatic monomericcompounds as carbon sources remain unidentified. Here, we employ a systems biology approach to elucidate the intracellular catabolism of vanillate – a monomethoxylated aromatic compound – in two white-rot fungi (WRF), Gelatoporia subvermispora and Trametes versicolor. We identified and biochemically validated a four-enzyme pathway that converts vanillate into ß-ketoadipate – a metabolite that enters central carbon metabolism. This pathway deviates from typical bacterial pathways, where vanillate is initially demethylated and ring-cleaved by intradiol dioxygenases; instead, oxidative decarboxylation occurs prior to ring cleavage by extradiol dioxygenases. Thus, we conducted an in-depth investigation of ring cleavage and further downstream catabolism by the identified fungal enzymes using biochemical and structural approaches. This revealed non-canonical enzymes, including a highly substrate-specific extradiol dioxygenase and a metal-free, promiscuous reductase, the latter capable of acting on catabolic intermediates derived from both methoxylated and non-methoxylated aromatic compounds. This work emphasizes the potential of WRF and their enzymes to advance lignin valorization and enhance our understanding of their role during wood decay.

dioxygenase↗
DOE OSTI2023

A cryptic oxidoreductase safeguards oxidative protein folding in Corynebacterium diphtheriae

In many gram-positive Actinobacteria, including Actinomyces oris and Corynebacterium matruchotii , the conserved thiol-disulfide oxidoreductase MdbA that catalyzes oxidative folding of exported proteins is essential for bacterial viability by an unidentified mechanism. Intriguingly, in Corynebacterium diphtheriae , the deletion of mdbA blocks cell growth only at 37 °C but not at 30 °C, suggesting the presence of alternative oxidoreductase enzyme(s). By isolating spontaneous thermotolerant revertants of the mdbA mutant at 37 °C, we obtained genetic suppressors, all mapped to a single T-to-G mutation within the promoter region of tsdA , causing its elevated expression. Strikingly, increased expression of tsdA —via suppressor mutations or a constitutive promoter—rescues the pilus assembly and toxin production defects of this mutant, hence compensating for the loss of mdbA . Structural, genetic, and biochemical analyses demonstrated TsdA is a membrane-tethered thiol-disulfide oxidoreductase with a conserved CxxC motif that can substitute for MdbA in mediating oxidative folding of pilin and toxin substrates. Together with our observation that tsdA expression is upregulated at nonpermissive temperature (40 °C) in wild-type cells, we posit that TsdA has evolved as a compensatory thiol-disulfide oxidoreductase that safeguards oxidative protein folding in C. diphtheriae against thermal stress.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Soil oxidoreductase zymography: Visualizing spatial distributions of peroxidase and phenol oxidase activities at the root-soil interface

Decomposition of organic material in the rhizosphere – the most dynamic microbial habitat in soil – involves arrays of oxidoreductase and hydrolytic enzymes. Spatial distributions of various hydrolytic activities in soil have already been explored by zymographic techniques. However, the distribution of oxidative activity in the rhizosphere remains to be studied. Thus, we extended a Time-Lapse Zymography technique, using Amplex Red® reagent, to visualize and quantify distributions of phenol oxidase and peroxidase activities in the rhizosphere of Zea mays L. growing in a Haplic Phaeozem and the non-rhizospheric soil. The gross oxidative activity was greatest at the root surfaces, and fell to background soil levels 1.26 and 0.73 mm from seminal (>1 mm diameter) and lateral (<0.5 mm diameter) roots, respectively. The rhizosphere extent relative to the root radius was 59% broader around lateral than around seminal roots. The greatest activities, up to 30 nmol cm –2 min –1 , were peroxidase-dominated and closely associated with roots. Here, the results confirm the utility of the approach for studying spatio-temporal distributions of oxidative activities in soil. However, actual activity of oxidoreductases in the field will be strongly controlled by fluctuating environmental conditions such as soil aeration and the gradient of reactive oxygen species, which need to be considered especially in anoxic soils.

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

Catalytic Bias of NADH-Dependent Reduced Ferredoxin: NADP+ Oxidoreductase (Nfn) and its Relevance to Ethanol Production in Thermoanaerobacterium Saccharolyticum

NADH-dependent reduced ferredoxin: NADP+ oxidoreductase (Nfn) enzyme catalyzes an energy-conserving flavin-based electron bifurcation (FBEB) reaction. In microbial metabolism, Nfn links redox pools of three electron carriers - ferredoxin (Fd), NAD(H), and NADP(H) - through the following FBEB reaction: 2 NADPH + NAD+ + 2 Fdox 2 NADP+ + NADH + 2 Fdred + H+ The forward reaction is termed electron bifurcation, and the reverse reaction is electron confurcation. Catalytic bias describes an enzyme's tendency to favor one direction of a reversible reaction over the other and is expressed as the ratio of activities in the two directions. Thermoanaerobacterium saccharolyticum (Tsac) is a thermophilic, ethanologenic bacterium that ferments hemicellulose to ethanol at yields above 90%. Its Nfn enzyme is known to support ethanol production, presumably by operating in the confurcating direction to balance cellular cofactors, but this has not previously been demonstrated. To investigate the Tsac Nfn further, we heterologously expressed, purified, and reconstituted the proteins NfnS (NfnA), NfnL (NfnB), and the putative partner Fd with iron-sulfur cluster and/or FAD cofactors. Activity assays monitoring the oxidation or reduction of Fd showed that, across pH 5-10, Tsac Nfn is catalytically biased towards the confurcating direction, favoring NADPH generation over NADPH oxidation by at least fivefold. Using protein electrochemistry, we also determined the reduction potentials of the cofactors in NfnL and Fd. These results indicate that the energetic landscape of FBEB in Tsac Nfn is similar to that in an ortholog. However, Tsac Fd has redox properties distinct from previously assayed Fds, suggesting that the identity and redox properties of Fd may help determine the catalytic bias of Nfn. Additionally, we confirmed the standalone ferredoxin: NADP+ oxidoreductase (FNOR) activity of NfnL but found it to be low and likely insignificant for in vivo redox conversion. We also show how the catalytic bias of Nfn integrates with the hydrogen cycling mechanism proposed in Tsac to better explain cofactor balancing for ethanol production. Our work advances the understanding of electron transfer processes within metabolic networks for the generation of valuable bioproducts.

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

A distinct class of ferredoxin:NADP + oxidoreductase enzymes driving thermophilic ethanol production

Biofuel production from lignocellulosic biomass offers a transformative solution to reduce global fossil fuel dependency. Certain thermophilic anaerobes, including Clostridium thermocellum, show promise for renewable ethanol production due to their ability to break down plant material at high temperatures. However, achieving commercially viable ethanol yields has proven challenging despite extensive engineering efforts. Here, we characterized 27 ferredoxin:NADP + oxidoreductase (Fnor) enzymes for their enzyme activity, nicotinamide cofactor specificity, thermotolerance, and functional expression in C. thermocellum . We identified a subset of 10 of these enzymes as a novel class of Fnor enzymes suited for metabolic pathways aimed at high-titer ethanol production. When expressed in engineered C. thermocellum , these enzymes increased ethanol production up to 2.2-fold. These findings establish a novel ethanol pathway and provide insights into physiological roles and biotechnological applications of this new class of Fnor enzymes.

09 BIOMASS FUELS↗
DOE OSTI2025

Insight Into the High-Potential Branch of the Alternate Nad+-Dependent NADPH:Ferredoxin Oxidoreductase II (NfnII) from Pyrococcus Furiosus. Evidence for the Gating Step in Electron Bifurcation

We have investigated the rapid-reaction kinetics of the NAD+-dependent NADPH:ferredoxin oxidoreductase II (NfnII) from Pyrococcus furiosus, permitting a comparison with recent work done with the paralog NfnI from the same organism. The half-potentials of the electron-bifurcating L-FAD are highly crossed in both NfnI, meaning the potential for the quinone/semiquinone couple is significantly lower than that for the semiquinone/hydroquinone couple so that the semiquinone oxidation state is thermodynamically unstable. The same appears to be the case with NfnII on the basis of its similar behavior in transient absorption spectroscopy experiments and the absence of any evidence for FAD*- accumulation in the course of reductive titrations (which would be manifested as a transient increase in absorbance at ~380 nm)1. Reductive titrations with both the one-electron donor sodium dithionite and the obligate two-electron donor NADPH demonstrate that, in contrast to NfnI, little FADH* accumulates in the high-potential pathway of NfnII in the course of reduction, as reflected in the absence of a transient increase in absorbance in the 500-600 nm region. This indicates that the half-potentials of the S-FAD are crossed in NfnII by a minimum of 120 mV. Rapid-reaction experiments mixing oxidized NfnII with NADPH also show no evidence of S-FADH* accumulation. Furthermore, the enzyme is only partially reduced at the end of the reaction with NADPH, indicating that there is little electron transfer into the high-potential pathway of NfnII. When the reaction is carried out in the presence of the one-electron carrier ferredoxin, only approximately one equivalent of ferredoxin becomes reduced, in contrast to the maximum of three equivalents seen with NfnI. This is consistent with only a single electron bifurcation event taking place under these conditions with NfnII, with only a single high-potential electron passing into the [2Fe-2S] cluster of the high-potential pathway of NfnII but not progressing further to the S-FAD. This accounts for the observation that NfnII has greatly reduced bifurcating activity compared to NfnI. The lack of electron transfer into the S-FAD of NfnII due to its crossed half-potentials prevents successive bifurcation activity and indicates that electron transfer within the high-potential branch gates bifurcation activity in NfnI.

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

Metalloprotein catalysis: structural and mechanistic insights into oxidoreductases from neutron protein crystallography

Metalloproteins catalyze a range of reactions, with enhanced chemical functionality due to their metal cofactor. The reaction mechanisms of metalloproteins have been experimentally characterized by spectroscopy, macromolecular crystallography and cryo-electron microscopy. An important caveat in structural studies of metalloproteins remains the artefacts that can be introduced by radiation damage. Photoreduction, radiolysis and ionization deriving from the electromagnetic beam used to probe the structure complicate structural and mechanistic interpretation. Neutron protein diffraction remains the only structural probe that leaves protein samples devoid of radiation damage, even when data are collected at room temperature. Additionally, neutron protein crystallography provides information on the positions of light atoms such as hydrogen and deuterium, allowing the characterization of protonation states and hydrogen-bonding networks. Neutron protein crystallography has further been used in conjunction with experimental and computational techniques to gain insight into the structures and reaction mechanisms of several transition-state metal oxidoreductases with iron, copper and manganese cofactors. Here, the contribution of neutron protein crystallography towards elucidating the reaction mechanism of metalloproteins is reviewed.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

What Makes a Bifurcase? Insights from a NADH-Dependent Reduced Ferredoxin: NADP+ Oxidoreductase (Nfn) and Homologs

NADH-dependent ferredoxin:NADP+ oxidoreductases (Nfn) is an enzyme family that engage in flavin-based electron bifurcation (FBEB), a mode of energy conservation utilized by life. The protein comprises one large (NfnL) and one small (NfnS) subunits. Thermoanaerobacterium sacchaloryticum (Tsac) is an anaerobic thermophilic bacterium that - with known involvement of Tsac Nfn - can produce ethanol in high, commercially viable concentrations. We sought to investigate the activity and energetic landscape of Tsac Nfn to determine how the enzyme effectuates FBEB. Tsac NfnS, NfnL, and the partner ferredoxin (Tsac Fd) were recombinantly expressed, purified, and reconstituted with iron-sulfur cluster and FAD cofactors. Electron paramagnetic resonance (EPR) was utilized for all proteins. Spectroelectrochemistry was performed with NfnL. Square-wave voltammetry was conducted on NfnL and Fd. Spectrophotometric activity was assayed for NfnL with or without NfnS. Our group continues to investigate the Nfn from Pyrococcus furiosus (Pf Nfn). Unlike Pf NfnS, Tsac NfnS can be stably expressed, purified, and reconstituted in the absence of its partner NfnL, allowing for this subunit to be characterized separately. The energetic profile of FBEB in Tsac Nfn is overall similar to that of Pf NfnL, with some differences: (1) the proximal cluster is at a lower potential (-780 mV vs -711), (2) the bifurcating FAD is at a higher potential (-406 mV vs -436 mV), and (3) Tsac Fd has two [4Fe-4S] clusters at -550 and -410 mV, unlike Pf Fd with a single cluster at approximately 400 mV. Activity assays indicate that the two enzymes perform FBEB in a similar way. Our work continues to build upon the new field of FBEB by demonstrating that the energetic landscape between distantly related archael (Pf) and bacterial (Tsac Nfn) are largely similar. This equips us to understand design principles for FBEB, allowing us to modulate the process in vivo for specific metabolic outcomes.

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

Cyclic Electron Flow-Coupled Proton Pumping in Synechocystis sp. PCC6803 Is Dependent upon NADPH Oxidation by the Soluble Isoform of Ferredoxin:NADP-Oxidoreductase

Ferredoxin:NADP-oxidoreductase (FNR) catalyzes the reversible exchange of electrons between ferredoxin (Fd) and NADP(H). Reduction of NADP+ by Fd via FNR is essential in the terminal steps of photosynthetic electron transfer, as light-activated electron flow produces NADPH for CO2 assimilation. FNR also catalyzes the reverse reaction in photosynthetic organisms, transferring electrons from NADPH to Fd, which is important in cyanobacteria for respiration and cyclic electron flow (CEF). The cyanobacterium Synechocystis sp. PCC6803 possesses two isoforms of FNR, a large form attached to the phycobilisome (FNRL) and a small form that is soluble (FNRS). While both isoforms are capable of NADPH oxidation or NADP+ reduction, FNRL is most abundant during typical growth conditions, whereas FNRS accumulates under stressful conditions that require enhanced CEF. Because CEF-driven proton pumping in the light–dark transition is due to NDH-1 complex activity and they are powered by reduced Fd, CEF-driven proton pumping and the redox state of the PQ and NADP(H) pools were investigated in mutants possessing either FNRL or FNRS. We found that the FNRS isoform facilitates proton pumping in the dark–light transition, contributing more to CEF than FNRL. FNRL is capable of providing reducing power for CEF-driven proton pumping, but only after an adaptation period to illumination. The results support that FNRS is indeed associated with increased cyclic electron flow and proton pumping, which is consistent with the idea that stress conditions create a higher demand for ATP relative to NADPH.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Understanding the stability of a plastic‐degrading Rieske iron oxidoreductase system

Abstract Rieske oxygenases (ROs) are a diverse metalloenzyme class with growing potential in bioconversion and synthetic applications. We postulated that ROs are nonetheless underutilized because they are unstable. Terephthalate dioxygenase (TPA DO PDB ID 7Q05 ) is a structurally characterized heterohexameric α 3 β 3 RO that, with its cognate reductase (TPA RED ), catalyzes the first intracellular step of bacterial polyethylene terephthalate plastic bioconversion. Here, we showed that the heterologously expressed TPA DO /TPA RED system exhibits only ~300 total turnovers at its optimal pH and temperature. We investigated the thermal stability of the system and the unfolding pathway of TPA DO through a combination of biochemical and biophysical approaches. The system's activity is thermally limited by a melting temperature ( T m ) of 39.9°C for the monomeric TPA RED , while the independent T m of TPA DO is 50.8°C. Differential scanning calorimetry revealed a two‐step thermal decomposition pathway for TPA DO with T m values of 47.6 and 58.0°C (Δ H = 210 and 509 kcal mol −1 , respectively) for each step. Temperature‐dependent small‐angle x‐ray scattering and dynamic light scattering both detected heat‐induced dissociation of TPA DO subunits at 53.8°C, followed by higher‐temperature loss of tertiary structure that coincided with protein aggregation. The computed enthalpies of dissociation for the monomer interfaces were most congruent with a decomposition pathway initiated by β‐β interface dissociation, a pattern predicted to be widespread in ROs. As a strategy for enhancing TPA DO stability, we propose prioritizing the re‐engineering of the β subunit interfaces, with subsequent targeted improvements of the subunits.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2003

Role of xanthine oxidoreductase and NAD(P)H oxidase in endothelial superoxide production in response to oscillatory shear stress

Oscillatory shear stress occurs at sites of the circulation that are vulnerable to atherosclerosis. Because oxidative stress contributes to atherosclerosis, we sought to determine whether oscillatory shear stress increases endothelial production of reactive oxygen species and to define the enzymes responsible for this phenomenon. Bovine aortic endothelial cells were exposed to static, laminar (15 dyn/cm2), and oscillatory shear stress (+/-15 dyn/cm2). Oscillatory shear increased superoxide (O2.-) production by more than threefold over static and laminar conditions as detected using electron spin resonance (ESR). This increase in O2*- was inhibited by oxypurinol and culture of endothelial cells with tungsten but not by inhibitors of other enzymatic sources. Oxypurinol also prevented H2O2 production in response to oscillatory shear stress as measured by dichlorofluorescin diacetate and Amplex Red fluorescence. Xanthine-dependent O2*- production was increased in homogenates of endothelial cells exposed to oscillatory shear stress. This was associated with decreased xanthine dehydrogenase (XDH) protein levels and enzymatic activity resulting in an elevated ratio of xanthine oxidase (XO) to XDH. We also studied endothelial cells lacking the p47phox subunit of the NAD(P)H oxidase. These cells exhibited dramatically depressed O2*- production and had minimal XO protein and activity. Transfection of these cells with p47phox restored XO protein levels. Finally, in bovine aortic endothelial cells, prolonged inhibition of the NAD(P)H oxidase with apocynin decreased XO protein levels and prevented endothelial cell stimulation of O2*- production in response to oscillatory shear stress. These data suggest that the NAD(P)H oxidase maintains endothelial cell XO levels and that XO is responsible for increased reactive oxygen species production in response to oscillatory shear stress.

NASA Discipline Cell Biology↗
DOE OSTI2022

Allosteric control of electron transfer in nitrogenase and nitrogenase-like enzymes (Final Report)

More than a third of all known proteins to date are either oxidoreductases or metalloproteins. The diversity of metal cofactors and redox centers in these proteins make them attractive candidates for engineering protein-based biocatalysts, biosensors, and biofuel cells, among other necessary tools for the bioeconomy. Many of these enzymes function as large multi-subunit complexes arranged as symmetric or asymmetric assemblies, and the purpose of this architecture is unclear. The goal of the project was to address this fundamental question by investigating the mechanism of action of two oxidoreductases: Nitrogenase and DPOR (Dark-Operative Protochlorophyllide Oxidoreductase, a nitrogenase-like oxidoreductase). Nitrogenase and DPOR play key roles in nitrogen fixation and photosynthesis, processes essential to sustaining life. Both proteins are arranged as two symmetrical halves with each half capable of substrate reduction. For more than half a century, substrate reduction by nitrogenase has been presumed to occur independently within the two identical halves. Funded by this DOE grant we have now shown that both nitrogenase and DPOR function asymmetrically. Electron transfer in one half suppresses activity in the other. Thus, we have demonstrated that the two halves do not function in an independent manner; rather, catalytic events in one-half allosterically suppress activity and electron transfer (ET) in the other. This alternating-site mechanism has significant implications on our current understanding of substrate reduction by these enzymes and offers a new mechanistic paradigm for the reactions they catalyze. Our work now provides a mechanistic map of the how the two symmetric catalytic halves work together to establish and maintain the sequential-site mechanism through multiple ET cycles to achieve substrate reduction. There is substantive need for bio-inspired tools that enable reduction of nitrogen and other substrates, as well as photosynthesis, for energy and food production. Understanding the workings of enzymes like nitrogenase and DPOR that mediate multi-electron redox chemistry is vital for designing such synthetic tools. The timing of our research coincides with the biotechnological breakthrough of light-driven artificial N2 reduction by nitrogenase, achieved using the native enzyme with both halves arranged in a mirror-like architecture as catalyst. Together with such discoveries, our research now reveal unknown facets of the reaction mechanism and hold promise for designing more effective catalysts.

59 BASIC BIOLOGICAL SCIENCES↗