NERNST: a genetically-encoded ratiometric non-destructive sensing tool to estimate NADP(H) redox status in bacterial, plant and animal systems

Nitrogen Assimilation Plays a Role in Balancing the Chloroplastic Glutathione Redox Potential Under High Light Conditions

Nitrate reduction requires reducing equivalents produced by the photosynthetic electron transport chain. Therefore, it has been suggested that nitrate assimilation provides a sink for electrons under high light conditions. We tested this hypothesis by monitoring photosynthetic efficiency and the chloroplastic glutathione redox potential (chl-EGSH) of plant lines with mutated glutamine synthetase 2 (GS2) and ferredoxin-dependent glutamate synthase 1 (GOGAT1). Mutant lines incorporated significantly less isotopically-labelled nitrate into amino acids than wild-type plants, demonstrating impaired nitrogen assimilation. When nitrate assimilation was compromised, photosystem II (PSII) proved more vulnerable to photodamage. The effect of the nitrate assimilation pathway on the chl- EGSH was monitored using the chloroplast-targeted roGFP2 biosensor (chl-roGFP2). Remarkably, while oxidation followed by reduction of chl-roGFP2 was detected in WT plants in response to high light, oxidation values were stable in the mutant lines, suggesting that chl-EGSH relaxation after high light-induced oxidation is achieved by diverting excess electrons to the nitrogen assimilation pathway. Importantly, similar ΦPSII and chl-roGFP2 patterns were observed at elevated CO2, suggesting that mutant phenotypes are not associated with photorespiration activity. Together, these findings indicate that the nitrogen assimilation pathway serves as a sustainable energy dissipation route, ensuring efficient photosynthetic activity and fine-tuning redox metabolism under light-saturated conditions.

DHRS7 Integrates NADP+/NADPH Redox Sensing with Inflammatory Lipid Signalling via the Oxoeicosanoid Pathway

During the innate immune response at epithelial wound sites, oxidative stress acts microbicidal and-mechanistically less well understood-as an immune and resilience signal. The reversible sulfhydryl (SH) oxidation of kinases, phosphatases, and transcription factors constitute the perhaps best-known redox signalling paradigm, whereas mechanisms that transduce metabolic redox cues, such as redox cofactor balance, remain little explored. Here, using mammalian cells, microsomes, and live zebrafish, we identify DHRS7, a short-chain fatty acid dehydrogenase/reductase (SDR), as conserved, 5-hydroxyeicosanoid dehydrogenase (5-HEDH). Under oxidative stress, DHRS7 consumes NADP+ to convert arachidonic acid (AA)-derived 5(S)-HETE into the inflammatory lipid 5-KETE, which activates leukocyte chemotaxis via the OXER1 receptor. While Dhrs7 acts as a NADPH-dependent 5-KETE sink in unstressed, healthy tissue, it promotes rapid, 5-KETE dependent leukocytic inflammation in wounded zebrafish skin. Thus, DHRS7 epitomizes an underappreciated mode of redox signalling-beyond classic SH oxidation-that leverages NADPH metabolism to generate or quench a paracrine lipid signal. Metabolic redox sensors like DHRS7 might be promising therapeutic targets in diseases characterized by disturbed redox balance.

A family of NADPH/NADP+ biosensors reveals in vivo dynamics of central redox metabolism across eukaryotes

The NADPH/NADP+ redox couple is central to metabolism and redox signalling. NADP redox state is differentially regulated by distinct enzymatic machineries at the subcellular compartment level. Nonetheless, a detailed understanding of subcellular NADP redox dynamics is limited by the availability of appropriate tools. Here, we introduce NAPstars, a family of genetically encoded, fluorescent protein-based NADP redox state biosensors. NAPstars offer real-time, specific measurements, across a broad-range of NADP redox states, with subcellular resolution. NAPstar measurements in yeast, plants, and mammalian cell models, reveal a conserved robustness of cytosolic NADP redox homoeostasis. NAPstars uncover cell cycle-linked NADP redox oscillations in yeast and illumination- and hypoxia-dependent NADP redox changes in plant leaves. By applying NAPstars in combination with selective impairment of the glutathione and thioredoxin antioxidative pathways under acute oxidative challenge, we find an unexpected and conserved role for the glutathione system as the primary mediator of antioxidative electron flux.

In vivo biosensing of subcellular pyruvate pools reveals photosynthesis-dependent metabolite dynamics in Nicotiana benthamiana

Pyruvate is central to metabolism across biology. It acts as a metabolic hub linking major pathways including glycolysis, the Krebs cycle, fermentation, and synthesis of amino acids, fatty acids, isoprenoids, and nucleotides. Even though the central role of pyruvate is well established biochemically, there is a remarkable gap in our understanding of how pyruvate levels behave within cells, where pyruvate is distributed across different compartments. Moreover, differential changes in pyruvate pools may occur rapidly upon changes in metabolic fluxes. Recently, this problem has been addressed by the development of a genetically encoded pyruvate biosensor to provide first insights into the pyruvate dynamics in animal cells. Here, we established in vivo biosensing of pyruvate in plants. We provided advanced characterization of the biosensor properties and demonstrated the functionality of the sensor in the cytosol, the mitochondria, and the chloroplasts of Nicotiana benthamiana epidermal cells. Finally, we harnessed the tool to investigate the impact of photosynthesis on pyruvate with unprecedented spatial and temporal resolution, revealing pronounced changes in subcellular pyruvate pools. While highlighting the current limitations of the biosensor, this study provides proof-of-concept for how the dynamics and regulation of central carbon metabolites can be revealed in living plant tissues.

Inside the microbial black box: a redox-centric framework for deciphering microbial metabolism

Microbial metabolism influences the global climate and human health and is governed by the balance between NADH and NAD+ through redox reactions. Historically, oxidative (i.e., catabolism) and reductive (i.e., fermentation) pathways have been studied in isolation, obscuring the complete metabolic picture. However, new omics technologies and biotechnological tools now allow an integrated system-level understanding of the drivers of microbial metabolism through observation and manipulation of redox reactions. Here we present perspectives on the importance of viewing microbial metabolism as the dynamic interplay between oxidative and reductive processes and apply this framework to diverse microbial systems. Additionally, we highlight novel biotechnologies to monitor and manipulate microbial redox status to control metabolism in unprecedented ways. This redox-focused systems biology framework enables a more mechanistic understanding of microbial metabolism.

Molecular Spies in Action: Genetically Encoded Fluorescent Biosensors Light up Cellular Signals

Cellular function is controlled through intricate networks of signals, which lead to the myriad pathways governing cell fate. Fluorescent biosensors have enabled the study of these signaling pathways in living systems across temporal and spatial scales. Over the years there has been an explosion in the number of fluorescent biosensors, as they have become available for numerous targets, utilized across spectral space, and suited for various imaging techniques. To guide users through this extensive biosensor landscape, we discuss critical aspects of fluorescent proteins for consideration in biosensor development, smart tagging strategies, and the historical and recent biosensors of various types, grouped by target, and with a focus on the design and recent applications of these sensors in living systems.

Real-time monitoring of stromal NADPH levels in Arabidopsis using a metagenome-derived NADPH-binding fluorescent protein

The light irradiation to the plant chloroplasts drives NADPH and ATP synthesis in the stroma via the electron transport chains within the thylakoid membranes. Conventional methods for assessing photosynthetic light reactions are often invasive or require specific conditions. While detection markers do not significantly affect plant growth itself, developing a method for the real-time and non-invasive detection of NADPH is a highly impactful and important research area in plant physiology and biochemistry. This study introduces a genetically encoded NADPH-binding blue fluorescent protein (mBFP) targeted to the chloroplast stroma or thylakoid membrane in Arabidopsis thaliana and Nicotiana benthamiana. Using two-photon microscopy, we monitored real-time stromal NADPH levels in transgenic leaves of Arabidopsis in response to light exposure. A mutant mBFP construct targeted to the thylakoid membrane allowed us to detect the stromal NADPH levels in real time under different light conditions. This in planta biosensor provides a non-invasive tool for studying photosynthetic responses to light more quantitatively and holds potential for optimizing light conditions in controlled-environment agriculture, such as indoor vertical farms, to improve crop productivity.

Thioredoxin System in Insects: Uncovering the Roles of Thioredoxins and Thioredoxin Reductase beyond the Antioxidant Defences

Increased levels of reactive oxygen species (ROS) produced during aerobic metabolism in animals can negatively affect the intracellular redox status, cause oxidative stress and interfere with physiological processes in the cells. The antioxidant defence regulates ROS levels by interplaying diverse enzymes and non-enzymatic metabolites. The thioredoxin system, consisting of the enzyme thioredoxin reductase (TrxR), the redox-active protein thioredoxin (Trx) and NADPH, represent a crucial component of antioxidant defence. It is involved in the signalling and regulation of multiple developmental processes, such as cell proliferation or apoptotic death. Insects have evolved unique variations of TrxR, which resemble mammalian enzymes in overall structure and catalytic mechanisms, but the selenocysteine-cysteine pair in the active site is replaced by a cysteine-cysteine pair typical of bacteria. Moreover, the role of the thioredoxin system in insects is indispensable due to the absence of glutathione reductase, an essential enzyme of the glutathione system. However, the functions of the Trx system in insects are still poorly characterised. In the present review, we provide a critical overview of the current knowledge on the insect Trx system, focusing mainly on TrxR's role in the antioxidant and immune system of model insect species.

Regulation of and challenges in targeting NAD+ metabolism

Nicotinamide adenine dinucleotide, in its oxidized (NAD+) and reduced (NADH) forms, is a reduction-oxidation (redox) co-factor and substrate for signalling enzymes that have essential roles in metabolism. The recognition that NAD+ levels fall in response to stress and can be readily replenished through supplementation has fostered great interest in the potential benefits of increasing or restoring NAD+ levels in humans to prevent or delay diseases and degenerative processes. However, much about the biology of NAD+ and related molecules remains poorly understood. In this Review, we discuss the current knowledge of NAD+ metabolism, including limitations of, assumptions about and unappreciated factors that might influence the success or contribute to risks of NAD+ supplementation. We highlight several ongoing controversies in the field, and discuss the role of the microbiome in modulating the availability of NAD+ precursors such as nicotinamide riboside (NR) and nicotinamide mononucleotide (NMN), the presence of multiple cellular compartments that have distinct pools of NAD+ and NADH, and non-canonical NAD+ and NADH degradation pathways. We conclude that a substantial investment in understanding the fundamental biology of NAD+, its detection and its metabolites in specific cells and cellular compartments is needed to support current translational efforts to safely boost NAD+ levels in humans.

Chloroplast thiol redox dynamics through the lens of genetically encoded biosensors

Chloroplasts fix carbon by using light energy and have evolved a complex redox network that supports plastid functions by (i) protecting against reactive oxygen species and (ii) metabolic regulation in response to environmental conditions. In thioredoxin- and glutathione/glutaredoxin-dependent redox cascades, protein cysteinyl redox steady states are set by varying oxidation and reduction rates. The specificity and interplay of these different redox-active proteins are still under investigation, for example to understand how plants cope with adverse environmental conditions by acclimation. Genetically encoded biosensors with distinct specificity can be targeted to subcellular compartments such as the chloroplast stroma, enabling in vivo real-time measurements of physiological parameters at different scales. These data have provided unique insights into dynamic behaviours of physiological parameters and redox-responsive proteins at several levels of the known redox cascades. This review summarizes current applications of different biosensor types as well as the dynamics of distinct protein cysteinyl redox steady states, with an emphasis on light responses.

Dynamic and Static Regulation of Nicotinamide Adenine Dinucleotide Phosphate: Strategies, Challenges, and Future Directions in Metabolic Engineering

Reduced nicotinamide adenine dinucleotide phosphate (NADPH) is a crucial cofactor in metabolic networks. The efficient regeneration of NADPH is one of the limiting factors for productivity in biotransformation processes. To date, many metabolic engineering tools and static regulation strategies have been developed to regulate NADPH regeneration. However, traditional static regulation methods often lead to the NADPH/NADP+ imbalance, causing disruptions in cell growth and production. These methods also fail to provide real-time monitoring of intracellular NADP(H) or NADPH/NADP+ levels. In recent years, various biosensors have been developed for the detection, monitoring, and dynamic regulate of the intracellular NADP(H) levels or the NADPH/NADP+ balance. These NADPH-related biosensors are mainly used in the cofactor engineering of bacteria, yeast, and mammalian cells. This review analyzes and summarizes the NADPH metabolic regulation strategies from both static and dynamic perspectives, highlighting current challenges and potential solutions, and discusses future directions for the advanced regulation of the NADPH/NADP+ balance.

A guide to genetically-encoded redox biosensors: State of the art and opportunities

Genetically-encoded redox biosensors have become invaluable tools for monitoring cellular redox processes with high spatiotemporal resolution, coupling the presence of the redox-active analyte with a change in fluorescence signal that can be easily recorded. This review summarizes the available fluorescence recording methods and presents an in-depth classification of the redox biosensors, organized by the analytes they respond to. In addition to the fluorescent protein-based architectures, this review also describes the recent advances on fluorescent, chemigenetic-based redox biosensors and other emerging chemigenetic strategies. This review examines how these biosensors are designed, the biosensors sensing mechanism, and their practical advantages and disadvantages.

Imaging immunometabolism in situ in live animals

Immunometabolism is a rapidly developing field that holds great promise for diagnostic and therapeutic benefits to human diseases. The field has emerged based on seminal findings from in vitro and ex vivo studies that established the fundamental role of metabolism in immune cell effector functions. Currently, the field is acknowledging the necessity of investigating cellular metabolism within the natural context of biological processes. Examining cells in their native microenvironment is essential not only to reveal cell-intrinsic mechanisms but also to understand how cross-talk between neighboring cells regulates metabolism at the tissue level in a local niche. This necessity is driving innovation and advancement in multiple imaging-based technologies to enable analysis of dynamic intracellular metabolism at the single-cell level, with spatial and temporal resolution. In this review, we tally the currently available imaging-based technologies and explore the emerging methods of Raman and autofluorescence lifetime imaging microscopy, which hold significant potential and offer broad applications in the field of immunometabolism.

In planta imaging of pyridine nucleotides using second-generation fluorescent protein biosensors

Redox changes of pyridine nucleotides in cellular compartments are highly dynamic and their equilibria are under the influence of various reducing and oxidizing reactions. To obtain spatiotemporal data on pyridine nucleotides in living plant cells, typical biochemical approaches require cell destruction. To date, genetically encoded fluorescent biosensors are considered to be the best option to bridge the existing technology gap, as they provide a fast, accurate, and real-time readout. However, the existing pyridine nucleotides genetically encoded fluorescent biosensors are either sensitive to pH change or slow in dissociation rate. Herein, we employed the biosensors which generate readouts that are pH stable for in planta measurement of NADH/NAD+ ratio and NADPH level. We generated transgenic Arabidopsis lines that express these biosensors in plastid stroma and cytosol of whole plants and pollen tubes under the control of CaMV 35S and LAT52 promoters, respectively. These transgenic biosensor lines allow us to monitor real-time dynamic changes in NADH/NAD+ ratio and NADPH level in the plastids and cytosol of various plant tissues, including pollen tubes, root hairs, and mesophyll cells, using a variety of fluorescent instruments. We anticipate that these valuable transgenic lines may allow improvements in plant redox biology studies.

Modern optical approaches in redox biology: Genetically encoded sensors and Raman spectroscopy

The objective of the current review is to summarize the current state of optical methods in redox biology. It consists of two parts, the first is dedicated to genetically encoded fluorescent indicators and the second to Raman spectroscopy. In the first part, we provide a detailed classification of the currently available redox biosensors based on their target analytes. We thoroughly discuss the main architecture types of these proteins, the underlying engineering strategies for their development, the biochemical properties of existing tools and their advantages and disadvantages from a practical point of view. Particular attention is paid to fluorescence lifetime imaging microscopy as a possible readout technique, since it is less prone to certain artifacts than traditional intensiometric measurements. In the second part, the characteristic Raman peaks of the most important redox intermediates are listed, and examples of how this knowledge can be implemented in biological studies are given. This part covers such fields as estimation of the redox states and concentrations of Fe-S clusters, cytochromes, other heme-containing proteins, oxidative derivatives of thiols, lipids, and nucleotides. Finally, we touch on the issue of multiparameter imaging, in which biosensors are combined with other visualization methods for simultaneous assessment of several cellular parameters.

Systemic and strict regulation of the glutathione redox state in mitochondria and cytosol is needed for zebrafish ontogeny

BACKGROUND

Redox control seems to be indispensable for proper embryonic development. The ratio between glutathione (GSH) and its oxidized disulfide (GSSG) is the most abundant cellular redox circuit.

METHODS

We used zebrafish harboring the glutaredoxin 1-redox sensitive green fluorescent protein (Grx1-roGFP) probe either in mitochondria or cytosol to test the hypothesis that the GSH:GSSG ratio is strictly regulated through zebrafish embryogenesis to sustain the different developmental processes of the embryo.

RESULTS

Following the GSSG:GSH ratio as a proxy for the GSH-dependent reduction potential (EhGSH) revealed increasing mitochondrial and cytosolic EhGSH during cleavage and gastrulation. During organogenesis, cytosolic EhGSH decreased, while that of mitochondria remained high. The similarity between EhGSH in brain and muscle suggests a central regulation. Modulation of GSH metabolism had only modest effects on the GSSG:GSH ratios of newly hatched larvae. However, inhibition of GSH reductase directly after fertilization led to dead embryos already 10 h later. Exposure to the emerging environmental pollutant Perfluorooctane Sulfonate (PFOS) disturbed the apparent regulated EhGSH as well.

CONCLUSIONS

Mitochondrial and cytosolic GSSG:GSH ratios are almost identical in different organs during zebrafish development indicating that the EhGSH might follow H2O2 levels and rather indirectly affect specific enzymatic activities needed for proper embryogenesis.

GENERAL SIGNIFICANCE

Our data confirm that vertebrate embryogenesis depends on strictly regulated redox homeostasis. Disturbance of the GSSG:GSH circuit, e.g. induced by environmental pollution, leads to malformation and death.