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Vol 90, No 12 (2025)

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EDITORIAL NOTES

Biochemistry. 2025;90(12):1901
pages 1901 views

MICROBIAL 2-ENOATE REDUCTASES CONTAINING A COVALENTLY BOUND FLAVIN MONONUCLEOTIDE

Bogachev A.V., Baykov A.A., Anashkin V.A., Bertsova Y.V.

Abstract

FMN and FAD are prosthetic groups of many enzymes and can be attached to proteins both covalently and non-covalently. Covalent attachment of FMN to Thr or Ser residues via a phosphate group is catalyzed by the recently discovered enzyme flavin transferase. Among the enzymes containing phosphoester-linked FMN, the most widely represented are various microbial 2-enoate reductases catalyzing the reduction of unsaturated carboxylic acids such as fumaric, acrylic, cinnamic, urocanic, and others. This review is focused on these enzymes and discusses their types by domain organization and intracellular localization, structural basis of substrate specificity, catalytic mechanism, role, as well as the significance and evolutionary origin of the covalent attachment of FMN as a prosthetic group.
Biochemistry. 2025;90(12):1902–1916
pages 1902–1916 views

MITOCHONDRIAL PERMEABILITY TRANSITION PORE: STRUCTURE, PROPERTIES AND ROLE IN CELLULAR PATHOPHYSIOLOGY

Belosludtsev K.N., Dubinin M.V., Belosludtseva N.V.

Abstract

The Mitochondrial Permeability Transition pore (MPT pore) activated by Ca2+ ions is a phenomenon that has long been the subject of intense study. Cyclophilin D-dependent opening of the MPT pore in mitochondria in response to calcium overload and oxidative stress leads to swelling of the mitochondrial matrix and depolarization of the inner membrane. These processes are accompanied by a dysregulation of ion homeostasis, damage to mitochondrial membranes and, ultimately, cell death. Despite decades of research, the molecular identity of the MPT pore remains unclear. Recently, its key structural components, along with the regulatory protein cyclophilin D, are considered to be the inner membrane proteins ATP synthase and adenine nucleotide translocator (ANT). The involvement of the MPT pore in the progression of various pathological conditions and diseases, as well as in a number of physiological processes, such as the regulation of cellular bioenergetics and rapid release of Ca2+, is widely discussed. This review summarizes modern molecular genetic data on the putative structure of the MPT pore, traces the evolution of views on its functioning — from the interpretation as a simple experimental artifact to the recognition of a putative key regulator of energy metabolism — and also considers the mechanisms of its regulation and pathophysiological role.
Biochemistry. 2025;90(12):1917–1940
pages 1917–1940 views

CLASSIFICATION OF MITOCHONDRIAL PROTONOPHORIC UNCOUPLERS AND THEIR MODIFICATIONS IN BIOLOGICAL ENVIRONMENT

Antonenko Y.N.

Abstract

This review is devoted to an analysis of the diversity of mitochondrial uncouplers, a class of compounds that Vladimir Petrovich Skulachev paid primary attention to throughout his scientific career, from the foundations of bioenergetics and the proof of the validity of Mitchell's chemiosmotic theory to the development of the concept of mild uncoupling and its therapeutic role. The review puts forward for the first time the idea of classifying uncouplers according to the type of functional group that provides their protonophoric activity, i.e., the ability to transfer protons across the membrane, causing its depolarization and thus uncoupling the work of proton pumps in the electron transport chain and ATP synthesis. In particular, it is shown that anionic and zwitterionic uncouplers can be divided into groups of OH-, NH-, SH- and CH-acids. An important aspect of this review is the consideration of metabolic transformations of mitochondrial uncouplers that determine the tissue specificity of their action.
Biochemistry. 2025;90(12):1941–1980
pages 1941–1980 views

ANTIBIOTICS AND CELLULAR SENESCENCE: AN UNEXPLORED TERRITORY

Zinovkin R.A., Kondratenko N.D.

Abstract

Antibiotics are certainly the most important agents in the fight against human and animal bacterial infections. The widespread use of antibiotics has a positive impact on the treatment of infectious diseases but may be accompanied by serious side effects. The clinical aspects of these side effects are well understood, but the nonspecific molecular targets are not fully recognized. It is generally known that many antibiotics can damage mitochondria, intracellular organelles responsible for aerobic metabolism as well as regulating a number of important processes, including cellular redox balance and inflammatory responses. Mitochondrial dysfunction commonly leads to the development of oxidative stress and inflammation, known stimuli of cellular senescence. On the other hand, the same stimuli can induce death of senescent cells. Thus, mitotoxic antibiotics may influence both the cellular senescence process and the elimination of senescent cells. The effect of antitumor antibiotics on the induction of cell aging has been studied in detail, but the effect of antibacterial antibiotics on this process is still essentially unknown. This review aims to draw researchers' attention to the possibility of accelerated cellular aging induced by common antibacterial antibiotics and to discuss the potential mechanisms behind this phenomenon.
Biochemistry. 2025;90(12):1981-1996
pages 1981-1996 views

CURRENT CHALLENGES AND FUTURE DIRECTIONS IN MITOCHONDRIAL POTASSIUM TRANSPORT RESEARCH

Nesterov S.V., Smirnova E.G., Yaguzhinsky L.S.

Abstract

Maintenance of ionic homeostasis, particularly the balance of potassium ions as the major cations in the cytoplasm, is critically important for mitochondrial function. Uncontrolled cation influx and the subsequent osmotically-driven water accumulation in the matrix can lead to swelling and eventual membrane rupture. Paradoxically, despite the critical importance of potassium channels and exchangers and their extensive research history, the molecular identity of key potassium transport systems such as the K+/H+ exchanger and the ATP-dependent potassium channel remains a subject of ongoing debate. Within this review and analysis of scientific publications, we outline a number of unresolved questions related to potassium transport in mitochondria: the incomplete knowledge of structural and functional rearrangements in mitochondria upon potassium ion influx and swelling; the ambiguity surrounding the molecular identity of key potassium transport systems — the K+/H+ exchanger and the ATP-dependent potassium channel, as well as the uncertain role of ATP synthase in ion transport; and the apparent underestimation of the role of the lipid component of the membrane in direct potassium transport and its regulation. We highlight that the accumulation of lysocardiolipin, a derivative of the key mitochondrial lipid cardiolipin, in the membrane may represent a missing link crucial for constructing a comprehensive explanation of mitochondrial osmotic regulation mechanisms. Lysocardiolipin can form lipid pores that significantly enhance membrane conductance for cations. The accumulation of lysocardiolipin can be stimulated by lipid peroxidation, alter membrane properties, and modulate the assembly and function of proteinaceous ion transporters. Accounting for changes in the physical (pressure, lipid packing) and chemical properties of the membrane (peroxidation, deacylation) during conditions that activate osmotic regulation systems is necessary for forming a holistic understanding of potassium transport mechanisms.
Biochemistry. 2025;90(12):1997—2011
pages 1997—2011 views

FROM CELLULAR ARCHITECTURE TO THE REGULATION OF MITOCHONDRIAL FUNCTION: THE ROLE OF VIMENTIN IN ENSURING CELLULAR MITOSTASIS

Deeb R., Shakhov A.S., Churkina A.S., Alieva I.B., Minin A.A.

Abstract

Mitochondria play a central role in cell physiology, and in addition to performing their primary function as an energy source, they are involved in processes such as regulating intracellular calcium levels, generating reactive oxygen species, synthesizing many critical compounds, regulating apoptosis, and more. In this regard, maintaining them in a normal state is of great importance, ensuring their transport, intracellular distribution, timely biogenesis, and removal of damaged mitochondria from cells. All of this is defined as cellular mitosis, the maintenance of which involves many cellular structures and, primarily, the cytoskeleton. This review summarizes data on the role of one component of the cytoskeleton, vimentin intermediate filaments, in these processes.
Biochemistry. 2025;90(12):2012—2020
pages 2012—2020 views

MECHANISMS UNDERLYING INTRACELLULAR SELECTION OF MITOCHONDRIAL DNA

Muravyov G., Knorre D.A.

Abstract

Different mtDNA variants can coexist within a single cell in a state of heteroplasmy, competing for the cellular resources necessary for their replication. In this review, we examine documented cases of selfish mitochondrial DNAs — variants that gain a replication advantage within cells but are detrimental at the cellular level — across a range of eukaryotic species, from humans to baker's yeast. This review discusses hypothetical mechanisms that may promote the proliferation of specific mtDNA variants over others in the heteroplasmic cells. Finally, we suggest that the risk posed by selfish mtDNAs has significantly shaped eukaryotic evolution, leading to the emergence of uniparental inheritance and constraints on mtDNA copy number.
Biochemistry. 2025;90(12):2021—2031
pages 2021—2031 views

ATP IN MITOCHONDRIA: QUANTITATIVE MEASUREMENT, REGULATION, AND PHYSIOLOGICAL ROLE

Lapashina A.S., Tretyakov D.O., Feniouk B.A.

Abstract

Oxidative phosphorylation in mitochondria is the main source of ATP in most eukaryotic cells. Concentrations of ATP, ADP, and AMP affect numerous cellular processes, including macromolecule biosynthesis, cell division, motor protein activity, ion homeostasis, and metabolic regulation. Variations in ATP levels also influence concentration of free Mg2+, thereby extending the range of affected reactions. In the cytosol, adenine nucleotide concentrations are relatively constant and typically are around 5 mM ATP, 0.5 mM ADP, and 0.05 mM AMP. These concentrations are mutually constrained by adenylate kinases operating in the cytosol and intermembrane space and are further linked to mitochondrial ATP and ADP pools via the adenine nucleotide translocator. Quantitative data on absolute adenine nucleotide concentrations in the mitochondrial matrix are limited. Total adenine nucleotide concentration lies in the millimolar range, but the matrix ATP/ADP ratio is consistently lower than the cytosolic ratio. Estimates of nucleotide fractions show substantial variability (ATP 20–75%, ADP 20–70%, AMP 3–60%), depending on the organism and experimental conditions. These observations suggest that the 'state 4' — inhibition of oxidative phosphorylation in the resting cells due to the low matrix ADP and elevated proton motive force that impedes respiratory chain activity — is highly unlikely in vivo. In this review, we discuss proteins regulating ATP levels in mitochondria and cytosol, consider experimental estimates of adenine nucleotide concentrations across a range of biological systems, and examine the methods used for their quantification, with particular emphasis on the genetically encoded fluorescent ATP sensors such as ATeam, QUEEN, and MaLion.
Biochemistry. 2025;90(12):2032-2048
pages 2032-2048 views

EXAMINATION OF THE REACTION OF CYTOCHROME bd-I OF Escherichia coli IN THE FULLY REDUCED STATE WITH CYANIDE USING ABSORPTION AND CIRCULAR DICHROISM SPECTROSCOPY

Borisov V.B., Arutyunyan A.M.

Abstract

We have previously begun to investigate the reaction of the isolated solubilized dithionite-reduced cytochrome bd-I of Escherichia coli with cyanide [Borisov and Arutyunyan (2024) J. Inorg. Biochem., 259, 112653]. The present work is a continuation of this study. The following new results were obtained using absorption and CD spectroscopy. 1) The membrane form of the fully reduced (FR) enzyme is also capable of binding cyanide. The apparent dissociation constant and second-order rate constant values are 81.1 ± 7.8 mM KCN and 0.11 ± 0.01 M-1·s-1, respectively. This contradicts the data of other researchers according to which the bd-I oxidase, located in native membranes, in FR-state does not bind cyanide. 2) CO added to the cyano adduct of both membrane and isolated solubilized forms of FR-cytochrome bd-I displaces cyanide, resulting in the formation of a complex of the enzyme with CO. This indicates the reversibility of cyanide binding to the protein. To saturate the oxidase binding site with CO in the presence of 100 mM KCN, much more CO is required than in the case of addition of CO to the enzyme that was not pre-treated with cyanide. CO and cyanide compete with each other for binding to the same site in the oxidase — heme d2+, and CO, being a stronger ligand, wins the competition with cyanide. 3) The effect of cyanide on the optical activity of FR-cytochrome bd-I was studied. The CD spectra of FR-enzyme obtained before and after cyanide treatment indicate that the formation of the cyano adduct of heme d2+ leads to a significant weakening of the excitonic interactions between heme d2+ and heme b5952+. Schemes of interaction of cyanide and CO in the presence of excess cyanide with the active center of FR-enzyme are proposed.
Biochemistry. 2025;90(12):2049-2062
pages 2049-2062 views

MITOCHONDRIAL RETICULUM OF SKELETAL MUSCLES. PROVEN AND HYPOTHETICAL FUNCTIONS

Bakeeva L.E., Vays V.B., Vangeli I.M., Eldarov C.M., Popkov V.A., Zorova L.D., Zorov S.D., Zorov D.B.

Abstract

In the 70s and 80s of the last century, the presence of the mitochondrial reticulum in skeletal muscles has been outlined. The concept functioning this reticulum in a cell to deliver energy throughout the cell volume in the form of a transmembrane potential built on the inner membrane of mitochondria, followed by the synthesis of ATP by mitochondrial ATP synthase, was put forth and proved. However, evidence based on studies of mitochondrial ultrastructure remains subject to criticism. To exclude the possibility of artifacts caused by the preparation of the sample for electron microscopy, the mitochondrial structure detected in ultrathin sections of muscle fiber used in electron microscopy and the structure in intact fiber were compared with the visualization of mitochondria with a membrane potential- dependent dye. This comparison was carried out for two species: mice and the naked mole rat, known for its extraordinary longevity. Full compliance with the previously made conclusions about the structure of the mitochondrial reticulum has been obtained. An additional model of the functioning of giant mitochondria as intracellular structures that prevent hypoxia in tissues is proposed.
Biochemistry. 2025;90(12):2063–2076
pages 2063–2076 views

PROGEROID SYNDROME WITH SIGNS OF AUTOPHAGY DYSFUNCTION IN THE NAKED MOLE RAT (Heterocephalus glaber)

Mansikkh V.N., Sheval E.V., Marey M.V., Averina O.A., Vyssokhik M.Y.

Abstract

The naked mole rat is considered a unique non-aging animal species and is widely used in laboratories to study lifespan biology. Previously, our group was the first to describe a new fatal disease of the naked mole rat, called "idiopathic cachexia". A detailed study of pathological changes in the organs of diseased animals together with data on changes in gene expression allows us to interpret this disease as a very specific variant of accelerated aging (progeroid syndrome or progeria) in these animals. Signs of the disease include cachexia, cataracts, lipofuscinosis and the appearance of amyloid bodies (corpora amylacea) in the brain, severe degeneration of myocardial cells, fatty degeneration and generalized lipofuscinosis of the liver and kidneys with signatures of dysfunction of autophagy processes in these organs. Further study is needed to elucidate the mechanism of development of this disease in animals with negligible aging, such as naked mole rats, and may have implications for understanding the mechanisms of aging and lifespan extension.
Biochemistry. 2025;90(12):2077–2092
pages 2077–2092 views

SUCCINATE CONFERS STRONGER CYTOPROTECTION IN KIDNEY CELLS THAN IN ASTROCYTES DUE TO ITS MORE EFFICIENT INVOLVEMENT IN ENERGY METABOLISM

Buyan M.I., Cherkesova K.S., Brezgunova A.A., Pevzner I.B., Andrianova N.V., Plotnikov E.Y.

Abstract

Being among the most metabolically active organs, brain and kidneys critically depend on efficient energy metabolism, which primarily relies on oxidative phosphorylation. Acute pathological conditions associated with a lack of metabolic substrates or their impaired utilization trigger signaling cascades that initiate cell death and lead to poorly reversible organ dysfunction. One of the therapeutic approaches to correct the energy deficit is administration of exogenous metabolites of the tricarboxylic acid cycle, such as succinate. In this study, we investigated the effects of exogenous succinate on astrocytes and renal epithelial cells under normal conditions and in serum deprivation-induced injury. Incubation with succinate increased the viability of both cell types under normal and pathological conditions, but a more pronounced cytoprotective effect was observed in renal cells. In injured renal epithelial cells, succinate increased mitochondrial membrane potential, a critical parameter for the maintenance of mitochondrial function and ATP generation. Comparison of respiration and oxidative phosphorylation parameters in astrocytes and renal epithelial cells in the presence of exogenous succinate revealed that epithelial cells exhibited a significantly higher respiratory control and lower proton leak compared to astrocytes, which correlated with the higher cytoprotective activity of succinate for kidney cells. Therefore, succinate showed a noticeable positive effect in the renal epithelium both under normal conditions and after serum deprivation; however, in astrocytes, its effect was less pronounced. This discrepancy might be related to a more efficient succinate utilization by the mitochondria in renal cells and intrinsic bioenergetic differences between astrocytes and epithelial cells. Despite the clinical use of succinate-containing drugs, the determination of optimal dosages and development of effective therapeutic regimens require further investigation. Our results demonstrate cell type-dependent differences in the efficacy of succinate, suggesting that its therapeutic potential may differ significantly depending on the organ-specific bioenergetic and metabolic properties.
Biochemistry. 2025;90(12):2093–2107
pages 2093–2107 views

MITOCHONDRIAL LIPID PEROXIDATION INITIATES RAPID ACCUMULATION OF LIPOFUSCIN IN CELL CULTURE

He H., Panteleeva A.A., Simonyan R.A., Avetisyan A.V., Lyamzaev K.G., Chernyak B.V.

Abstract

It was shown that the enhancement of lipid peroxidation (LPO) in mitochondria of rat H9c2 cardiomyoblasts and human fibroblasts under the action of the cystine transport inhibitor erastin or the glutathione peroxidase-4 inhibitor RSL3 is accompanied by rapid (18 h) accumulation of lipofuscin. The mitochondria-targeted antioxidant SkQ1 and the redox mediator methylene blue, which prevents the formation of reactive oxygen species (ROS) in complex I of the mitochondrial respiratory chain, blocked both mitochondrial LPO and lipofuscin accumulation. These data indicate that mitochondrial LPO serves as a driving force for the accelerated accumulation of lipofuscin in cells. In isolated heart mitochondria, rapid (24 h) formation of lipofuscin was observed, which depended on the presence of iron ions, was significantly accelerated by ROS generated in complex I of the respiratory chain, and was blocked by SkQ1. The question of whether oxidized components of mitochondria serve as the initial material for lipofuscin formation in cells remains open. The obtained results give hope for the successful application of mitochondria-targeted compounds in the treatment of many diseases associated with excessive accumulation of lipofuscin.
Biochemistry. 2025;90(12):2108–2118
pages 2108–2118 views

THE MECHANISMS AND PATHWAYS TO OVERCOME THE ACQUIRED RESISTANCE OF TUMOR CELLS TO Mcl-1 ANTAGONISTS

Pervushin N.V., Valdez Fernandez B.Y., Senichkin V.V., Yapryntseva M.A., Pavlov V.S., Zhivotovsky B., Kopeina G.S.

Abstract

Acquired drug resistance reduces the efficiency of cancer treatment and leads to cancer progression. The selective inhibition of antiapoptotic proteins from the Bcl-2 family by BH3 mimetics is a promising strategy for the treatment of cancer patients. In recent years, antagonists of the antiapoptotic protein Mcl-1 have been intensively studied in clinical trials; however, like other BH3 mimetics, they may lose their effectiveness due to the development of acquired resistance. We have found that tumor cells develop resistance to Mcl-1 inhibition due to increased expression of genes of other antiapoptotic proteins (Bcl-2 or Bcl-xL), becoming less Mcl-1-dependent. The development of this type of resistance can also be accompanied by changes in cell metabolism. We have shown that combining Mcl-1 antagonist S63845 and various antitumor compounds can lead to overcoming the resistance of malignant cells to its action.
Biochemistry. 2025;90(12):2119-2138
pages 2119-2138 views

MITOCHONDRIA IN DEVELOPING BRAIN: CONTRIBUTION OF DEVIATIONS TO HIGHER SUSCEPTIBILITY TO NEURODEGENERATION IN LATTER PERIODS OF LIFE

Stefanova N.A., Muraleva N.A., Sityaeva D.V., Tyumentsev M.A., Kolosova N.G.

Abstract

It has been proven that the preclinical period of the sporadic (> 95% of cases) form of Alzheimer's disease (AD) can last for decades, but the question of when the disease begins to develop and what contributes to it remains open. It is assumed that vulnerability to AD can be facilitated by the anatomical and functional parameters of the brain that form early in life. This is also supported by the results of our studies on accelerated senescence OXYS rats, a unique model of AD. The delay in brain maturation revealed in them is associated with insufficient glial support, a key regulator of neural network functioning, and the development of AD signs in OXYS rats is preceded and accompanied by mitochondrial dysfunction. This allowed us to raise the question of whether the structural and functional features of mitochondria can influence the process of brain maturation and thus determine the predisposition to the further development of AD signs. In this study, we compared mitochondrial biogenesis, their traffic and structural state in neuronal cell bodies, axonal and dendritic processes, and the activity of mitochondrial dynamics processes in the prefrontal cortex and hippocampus of OXYS and Wistar rats (control) during the period of brain maturation completion (from birth to 20 days of age). Changes in the number and ultrastructural parameters of mitochondria were compared with the activity of dynamics processes, which was assessed by the frequency of occurrence of mitochondria undergoing fusion or fission, the content of the key protein of their biogenesis PGC- 1a and proteins mediating mitochondrial dynamics (mitofusins MFN1 and MFN2, dynamin- 1- like protein DRP1). In OXYS rats, abnormalities in the formation of the mitochondrial apparatus in the early postnatal period were revealed, which can contribute to the delay in brain maturation of OXYS rats, promote mitochondrial dysfunction, decreased synapse density and, ultimately, neuronal death and the development of early neurodegenerative changes in the future.
Biochemistry. 2025;90(12):2139-2152
pages 2139-2152 views

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