Modification of Glyceraldehyde-3-Phosphate Dehydrogenase with Nitric Oxide: Role in Signal Transduction and Development of Apoptosis

Analysis of the High-Order Conformational Changes in Glyceraldehyde-3-phosphate Dehydrogenase Induced by Nicotinamide Adenine Dinucleotide, Adenosine Triphosphate, and Oxidants

Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a key enzyme in glycolysis. Beyond this normal function, GAPDH acts as a moonlighting protein, interacting with nonglycolytic molecules to fulfill additional roles, such as apoptosis induction. However, the three-dimensional (3D) structural details underlying these interactions remain unclear, likely due to their dynamic and transient nature. To address this issue, we investigated the structural properties of human and porcine GAPDH using a combination of biophysical techniques, including nuclear magnetic resonance (NMR) spectroscopy, mass spectrometry, gel filtration chromatography, and thermal shift assays, with a particular focus on their 3D structures. Our results revealed that although GAPDH becomes unstable upon nicotinamide adenine dinucleotide (NAD+) depletion (apo state), its oligomeric structure as a tetramer remains preserved regardless of temperature. In contrast, the presence of adenosine triphosphate (ATP) promotes dimerization at low temperatures, as previously reported. Furthermore, our NMR data suggest that ATP binding exposes the dimer interface and increases the flexibility of side chains in this region. These findings indicate that GAPDH maintains a stable tetrameric structure in the presence of NAD+ but becomes structurally unstable and likely more susceptible to oxidation upon NAD+ depletion. Additionally, our analyses showed that partial nitrosylation of GAPDH subunits does not induce significant tertiary structural changes. However, significant structural alterations were observed when all four subunits were nitrosylated, although the possibility remains that residues other than the active site residue, Cys152, may have been oxidized. We propose that NAD+ depletion, along with oxidation or nitrosylation─most likely at Cys152─destabilizes the GAPDH conformation, and that subsequent ATP binding promotes dimerization. This subunit dissociation may serve as a structural basis for GAPDH's interactions with other molecules and its moonlighting functions.

Multi-dimensional bio mass cytometry: simultaneous analysis of cytoplasmic proteins and metabolites on single cells

Single-cell multi-dimensional analysis enables more profound biological insight, providing a comprehensive understanding of cell physiological processes. Due to limited cellular contents, the lack of protein and metabolite amplification ability, and the complex cytoplasmic environment, the simultaneous analysis of intracellular proteins and metabolites remains challenging. Herein, we proposed a multi-dimensional bio mass cytometry platform characterized by protein signal conversion and amplification through an orthogonal exogenous enzymatic reaction. Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) gene editing technology was applied in the quantification of endogenous intracellular protein glycer-aldehyde-3-phosphate dehydrogenase (GAPDH) through exogenous luciferase Nanoluc (Nluc). The simultaneous detection of GAPDH and hundreds of metabolites at the single-cell level was realized for the first time. Semiquantitative analysis of GAPDH together with single-cell metabolomes under S-nitrosoglutathione (GSNO)-induced oxidative stress was investigated. Bioinformatics analysis revealed 16 metabolites that correlated positively with GAPDH expression upon oxidative stress, including long-chain fatty acids (palmitoleic acid, myristic acid, etc.) and UDP-N-acetylglucosamine (UDP-GlcNAc). Potential synergetic functions of GAPDH and UDP-GlcNAc-mediated oxidative stress responses were also elucidated. Our work proposes a novel strategy for the simultaneous quantitative analysis of single-cell intracellular proteins and metabolites, deepens the understanding of inherent anti-oxidative stress response mechanisms, and provides the molecular fundamentals for the study of inherent biological processes.

4-Hexylresorcinol Enhances Glut4 Expression and Glucose Homeostasis via AMPK Activation and Histone H3 Acetylation

This study investigates the potential of 4-hexylresorcinol (4HR) as a novel antidiabetic agent by assessing its effects on blood glucose levels, Glut4 expression, AMPK phosphorylation, and Histone H3 acetylation (Ac-H3) in the liver. In vitro experiments utilized Huh7 and HepG2 cells treated with varying concentrations of 4HR. Glut4, p-AMPK, and Ac-H3 expression levels were quantified via Western blotting. Additionally, GAPDH activity and glucose uptake were evaluated. In vivo experiments employed streptozotocin (STZ)-induced diabetic rats, with or without 4HR treatment, monitoring blood glucose, body weight, and hepatic levels of Glut4, p-AMPK, and Ac-H3. In vitro, 4HR treatment increased GAPDH activity and glucose uptake. Elevated Glut4, p-AMPK, and Ac-H3 levels were observed 8 h after 4HR administration. Inhibition of p-AMPK using compound C reduced 4HR-mediated Glut4 expression. In STZ-induced diabetic rats, 4HR significantly upregulated Glut4, p-AMPK, and Ac-H3 expression in the liver. Periodic 4HR injections mitigated weight loss and lowered blood glucose levels in STZ-injected animals. Histological analysis revealed increased glycogen storage in hepatocytes of the 4HR-treated group. Overall, 4HR enhanced Glut4 expression through upregulation of AMPK activity and histone H3 acetylation in vitro and in vivo, improving hepatic glucose homeostasis and suggesting potential as a candidate for diabetes treatment.

Binding of glyceraldehyde-3-phosphate dehydrogenase to G-actin promotes the transnitrosylation reaction

In this study, we investigated formation of the complex between glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and actin and the possibility of nitrosyl group transfer between GAPDH and actin. A complex of GAPDH with beta-actin was isolated from lysates of HEK293T cells using immunoprecipitation with antibodies against GAPDH or against beta-actin. The treatment of the cells with H2O2 or NO donor did not affect the formation of the complex. Investigation of the interaction between purified GAPDH and muscle alpha-actin showed that GAPDH interacts better with globular (G-) actin than with fibrillary actin, and oxidation/reduction of GAPDH does not affect this interaction. S-nitrosylated GAPDH (GAPDH-SNO) was partially reactivated in the presence of G-actin, which was accompanied by denitrosylation of GAPDH and sulfenation of G-actin. The sulfenated cysteine residue in G-actin was identified by MALDI-TOF MS analysis as C-terminal Cys374. Based on the properties of nitrosothiols, we assume that the cysteine-sulfenic acid in actin is a product of spontaneous hydrolysis of S-nitrosylated cysteine residue. The obtained results suggest that Cys374 in actin is S-nitrosylated during the incubation with GAPDH-SNO (transnitrosylation reaction). The transfer of the NO-group from GAPDH-SNO to the C-terminal Cys374 of actin suggests that upon interaction with GAPDH, the C-terminus of actin is located in the active center of GAPDH in the proximity to the catalytic Cys152. It is possible that the ability of GAPDH-SNO to nitrosylate actin contributes to the redox regulation of actin-controlled signaling pathways.

Supramolecular Protein Assemblies: Building Blocks, Organism- or Cell-Specific Varieties, and Significance

In recent decades, biology has made tremendous progress in the high-throughput analytic and genetic techniques used to characterize the molecular components of living cells and their interactions [...].

Targeting Metabolic-Redox Nexus to Regulate Drug Resistance: From Mechanism to Tumor Therapy

Drug resistance is currently one of the biggest challenges in cancer treatment. With the deepening understanding of drug resistance, various mechanisms have been revealed, including metabolic reprogramming and alterations of redox balance. Notably, metabolic reprogramming mediates the survival of tumor cells in harsh environments, thereby promoting the development of drug resistance. In addition, the changes during metabolic pattern shift trigger reactive oxygen species (ROS) production, which in turn regulates cellular metabolism, DNA repair, cell death, and drug metabolism in direct or indirect ways to influence the sensitivity of tumors to therapies. Therefore, the intersection of metabolism and ROS profoundly affects tumor drug resistance, and clarifying the entangled mechanisms may be beneficial for developing drugs and treatment methods to thwart drug resistance. In this review, we will summarize the regulatory mechanism of redox and metabolism on tumor drug resistance and highlight recent therapeutic strategies targeting metabolic-redox circuits, including dietary interventions, novel chemosynthetic drugs, drug combination regimens, and novel drug delivery systems.

S-nitrosylation and S-glutathionylation of GAPDH: Similarities, differences, and relationships

The aim of this work was to compare the effect of reversible post-translational modifications, S-nitrosylation and S-glutathionylation, on the properties of glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and to reveal the mechanism of the relationship between these modifications. Comparison of S-nitrosylated and S-glutathionylated GAPDH showed that both modifications inactivate the enzyme and change its spatial structure, decreasing the thermal stability of the protein and increasing its sensitivity to trypsin cleavage. Both modifications are reversible in the presence of dithiothreitol, however, in the presence of reduced glutathione and glutaredoxin 1, the reactivation of S-glutathionylated GAPDH is much slower (10% in 2 h) compared to S-nitrosylated GAPDH (60% in 10 min). This suggests that S-glutathionylation is a much less reversible modification compared to S-nitrosylation. Incubation of HEK 293 T cells in the presence of H₂O₂ or with the NO donor diethylamine NONOate results in accumulation of sulfenated GAPDH (by data of Western blotting) and S-glutathionylated GAPDH (by data of immunoprecipitation with anti-GSH antibodies). Besides GAPDH, a protein of 45 kDa was found to be sulfenated and S-glutathionylated in the cells treated with H₂O₂ or NO. This protein was identified as beta-actin. The results of this study confirm the previously proposed hypothesis based on in vitro investigations, according to which S-nitrosylation of the catalytic cysteine residue (Cys152) of GAPDH with subsequent formation of cysteine sulfenic acid at Cys152 may promote its S-glutathionylation in the presence of cellular GSH. Presumably, the mechanism may be valid in the case of beta-actin.

Regulation of Intersubunit Interactions in Homotetramer of Glyceraldehyde-3-Phosphate Dehydrogenases upon Its Immobilization in Protein-Kappa-Carrageenan Gels

Polysaccharides, being biocompatible and biodegradable polymers, are highly attractive as materials for protein delivery systems. However, protein-polysaccharide interactions may lead to protein structural transformation. In the current study, we analyze the structural adjustment of a homotetrameric protein, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), upon its interactions with both flexible coil chain and the rigid helix of κ-carrageenan. FTIR spectroscopy was used to probe the secondary structures of both protein and polysaccharide. Electrostatically driven protein-polysaccharide interactions in dilute solutions resulted in an insoluble complex formation with a constant κ-carrageenan/GAPDH ratio of 0.2, which amounts to 75 disaccharide units per mole of protein tetramer. Upon interactions with both coiled and helical polysaccharides, a weakening of the intersubunit interactions was revealed and attributed to a partial GAPDH tetramer dissociation. In turn, protein distorted the helical conformation of κ-carrageenan when co-gelled. Molecular modeling showed the energy favorable interactions between κ-carrageenan and GAPDH at different levels of oligomerization. κ-Carrageenan binds in the region of the NAD-binding groove and the S-loop in OR contact, which may stabilize the OP dimers. The obtained results highlight the mutual conformational adjustment of oligomeric GAPDH and κ-carrageenan upon interaction and the stabilization of GAPDH's dissociated forms upon immobilization in polysaccharide gels.

Expanding roles for S-nitrosylation in the regulation of plant immunity

Following pathogen recognition, plant cells produce a nitrosative burst resulting in a striking increase in nitric oxide (NO), altering the redox state of the cell, which subsequently helps orchestrate a plethora of immune responses. NO is a potent redox cue, efficiently relayed between proteins through its co-valent attachment to highly specific, powerfully reactive protein cysteine (Cys) thiols, resulting in formation of protein S-nitrosothiols (SNOs). This process, known as S-nitrosylation, can modulate the function of target proteins, enabling responsiveness to cellular redox changes. Key targets of S-nitrosylation control the production of reactive oxygen species (ROS), the transcription of immune-response genes, the triggering of the hypersensitive response (HR) and the establishment of systemic acquired resistance (SAR). Here, we bring together recent advances in the control of plant immunity by S-nitrosylation, furthering our appreciation of how changes in cellular redox status reprogramme plant immune function.

S-Glutathionylation and S-Nitrosylation in Mitochondria: Focus on Homeostasis and Neurodegenerative Diseases

Redox post-translational modifications are derived from fluctuations in the redox potential and modulate protein function, localization, activity and structure. Amongst the oxidative reversible modifications, the S-glutathionylation of proteins was the first to be characterized as a post-translational modification, which primarily protects proteins from irreversible oxidation. However, a growing body of evidence suggests that S-glutathionylation plays a key role in core cell processes, particularly in mitochondria, which are the main source of reactive oxygen species. S-nitrosylation, another post-translational modification, was identified >150 years ago, but it was re-introduced as a prototype cell-signaling mechanism only recently, one that tightly regulates core processes within the cell’s sub-compartments, especially in mitochondria. S-glutathionylation and S-nitrosylation are modulated by fluctuations in reactive oxygen and nitrogen species and, in turn, orchestrate mitochondrial bioenergetics machinery, morphology, nutrients metabolism and apoptosis. In many neurodegenerative disorders, mitochondria dysfunction and oxidative/nitrosative stresses trigger or exacerbate their pathologies. Despite the substantial amount of research for most of these disorders, there are no successful treatments, while antioxidant supplementation failed in the majority of clinical trials. Herein, we discuss how S-glutathionylation and S-nitrosylation interfere in mitochondrial homeostasis and how the deregulation of these modifications is associated with Alzheimer’s, Parkinson’s, amyotrophic lateral sclerosis and Friedreich’s ataxia.

Strategies of Pathogens to Escape from NO-Based Host Defense

Nitric oxide (NO) is an essential signaling molecule present in most living organisms including bacteria, fungi, plants, and animals. NO participates in a wide range of biological processes including vasomotor tone, neurotransmission, and immune response. However, NO is highly reactive and can give rise to reactive nitrogen and oxygen species that, in turn, can modify a broad range of biomolecules. Much evidence supports the critical role of NO in the virulence and replication of viruses, bacteria, protozoan, metazoan, and fungi, thus representing a general mechanism of host defense. However, pathogens have developed different mechanisms to elude the host NO and to protect themselves against oxidative and nitrosative stress. Here, the strategies evolved by viruses, bacteria, protozoan, metazoan, and fungi to escape from the NO-based host defense are overviewed.

Mechanism of GAPDH Redox Signaling by H2O2 Activation of a Two-Cysteine Switch

Oxidation of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) by reactive oxygen species such as H2O2 activate pleiotropic signaling pathways is associated with pathophysiological cell fate decisions. Oxidized GAPDH binds chaperone proteins with translocation of the complex to the nucleus and mitochondria initiating autophagy and cellular apoptosis. In this study, we establish the mechanism by which H2O2-oxidized GAPDH subunits undergo a subunit conformational rearrangement. H2O2 oxidizes both the catalytic cysteine and a vicinal cysteine (four residues downstream) to their respective sulfenic acids. A 'two-cysteine switch' is activated, whereby the sulfenic acids irreversibly condense to an intrachain thiosulfinic ester resulting in a major metastable subunit conformational rearrangement. All four subunits of the homotetramer are uniformly and independently oxidized by H2O2, and the oxidized homotetramer is stabilized at low temperatures. Over time, subunits unfold forming disulfide-linked aggregates with the catalytic cysteine oxidized to a sulfinic acid, resulting from thiosulfinic ester hydrolysis via the highly reactive thiosulfonic ester intermediate. Molecular Dynamic Simulations provide additional mechanistic insights linking GAPDH subunit oxidation with generating a putative signaling conformer. The low-temperature stability of the H2O2-oxidized subunit conformer provides an operable framework to study mechanisms associated with gain-of-function activities of oxidized GAPDH to identify novel targets for the treatment of neurodegenerative diseases.

AMP-activated protein kinase-dependent nuclear localization of glyceraldehyde 3-phosphate dehydrogenase in senescent human diploid fibroblasts

Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a key glycolytic enzyme that participates in various cellular events, such as DNA repair and apoptosis. The functional diversity of GAPDH depends on its intracellular localization. Because AMP-activated protein kinase (AMPK) regulates the nuclear translocation of GAPDH in young cells and AMPK activity significantly increases during aging, we investigated whether altered AMPK activity is involved in the nuclear localization of GAPDH in senescent cells. Age-dependent nuclear translocation of GAPDH was confirmed by confocal laser scanning microscopy in human diploid fibroblasts (HDFs) and by immunohistochemical analysis in aged rat skin cells. Senescence-induced nuclear localization was reversed by lysophosphatidic acid but not by platelet-derived growth factor. The extracellular matrix from young cells also induced the nuclear export of GAPDH in senescent HDFs. An activator of AMPK, 5-Aminoimidazole-4-carboxamide-1-β-D-ribofuranoside (AICAR), increased the level of nuclear GAPDH, whereas an inhibitor of AMPK, Compound C, decreased the level of nuclear GAPDH in senescent HDFs. Transfection with AMPKα siRNA prevented nuclear translocation of GAPDH in senescent HDFs. The stimulatory effect of AICAR and serum depletion on GAPDH nuclear translocation was reduced in AMPKα1/α2-knockout mouse embryonic fibroblasts. Overall, increased AMPK activity may play a role in the senescence-associated nuclear translocation of GAPDH.