bims-minimp 2022-05-29 papers

on Mitochondria, innate immunity, proteostasis

Issue of 2022–05–29
fiveteen papers selected by
Hanna Salmonowicz, International Institute of Molecular Mechanisms and Machines of the Polish Academy of Sciences

DRP1 levels determine the apoptotic threshold during embryonic differentiation through a mitophagy-dependent mechanism.
Defining mitochondrial protein functions through deep multiomic profiling.
Genetic screen identifies non-mitochondrial proteins involved in the maintenance of mitochondrial homeostasis.
Defective mitophagy in aged macrophages promotes mitochondrial DNA cytosolic leakage to activate STING signaling during liver sterile inflammation.
Mitochondrial respiratory chain protein co-regulation in the human brain.
Disruption of the MICOS complex leads to an aberrant cristae structure and an unexpected, pronounced lifespan extension in Podospora anserina.
The UPRmt preserves mitochondrial import to extend lifespan.
Mitochondrial thioredoxin system is required for enhanced stress resistance and extended longevity in long-lived mitochondrial mutants.
Triplication of HSA21 on alterations in structure and function of mitochondria.
A new hope: Mitochondria, a critical factor in the war against prions.
The mitochondrial chaperone TRAP1 regulates F-ATP synthase channel formation.
Senescence-induced endothelial phenotypes underpin immune-mediated senescence surveillance.
Money, power, and mitochondria.
The heterogeneity of cellular senescence: insights at the single-cell level.
Supercomplex supercomplexes: Raison d'etre and functional significance of supramolecular organization in oxidative phosphorylation.

Dev Cell. 2022 May 15. pii: S1534-5807(22)00306-9. [Epub ahead of print]

DRP1 levels determine the apoptotic threshold during embryonic differentiation through a mitophagy-dependent mechanism.

Barbara Pernaute, Salvador Pérez-Montero, Juan Miguel Sánchez Nieto, Aida Di Gregorio, Ana Lima, Katerina Lawlor, Sarah Bowling, Gianmaria Liccardi, Alejandra Tomás, Pascal Meier, Hiromi Sesaki, Guy A Rutter, Ivana Barbaric, Tristan A Rodríguez.

  The changes that drive differentiation facilitate the emergence of abnormal cells that need to be removed before they contribute to further development or the germline. Consequently, in mice in the lead-up to gastrulation, ∼35% of embryonic cells are eliminated. This elimination is caused by hypersensitivity to apoptosis, but how it is regulated is poorly understood. Here, we show that upon exit of naive pluripotency, mouse embryonic stem cells lower their mitochondrial apoptotic threshold, and this increases their sensitivity to cell death. We demonstrate that this enhanced apoptotic response is induced by a decrease in mitochondrial fission due to a reduction in the activity of dynamin-related protein 1 (DRP1). Furthermore, we show that in naive pluripotent cells, DRP1 prevents apoptosis by promoting mitophagy. In contrast, during differentiation, reduced mitophagy levels facilitate apoptosis. Together, these results indicate that during early mammalian development, DRP1 regulation of mitophagy determines the apoptotic response.

Keywords:  apoptosis; early development; embryonic stem cell differentiation; mitochondrial dynamics; mitophagy; pluripotency

DOI:  https://doi.org/10.1016/j.devcel.2022.04.020
Nature. 2022 May 25.

Defining mitochondrial protein functions through deep multiomic profiling.

Jarred W Rensvold, Evgenia Shishkova, Yuriy Sverchkov, Ian J Miller, Arda Cetinkaya, Angela Pyle, Mateusz Manicki, Dain R Brademan, Yasemin Alanay, Julian Raiman, Adam Jochem, Paul D Hutchins, Sean R Peters, Vanessa Linke, Katherine A Overmyer, Austin Z Salome, Alexander S Hebert, Catherine E Vincent, Nicholas W Kwiecien, Matthew J P Rush, Michael S Westphall, Mark Craven, Nurten A Akarsu, Robert W Taylor, Joshua J Coon, David J Pagliarini.

Mitochondria are epicentres of eukaryotic metabolism and bioenergetics. Pioneering efforts in recent decades have established the core protein componentry of these organelles1 and have linked their dysfunction to more than 150 distinct disorders2,3. Still, hundreds of mitochondrial proteins lack clear functions4, and the underlying genetic basis for approximately 40% of mitochondrial disorders remains unresolved5. Here, to establish a more complete functional compendium of human mitochondrial proteins, we profiled more than 200 CRISPR-mediated HAP1 cell knockout lines using mass spectrometry-based multiomics analyses. This effort generated approximately 8.3 million distinct biomolecule measurements, providing a deep survey of the cellular responses to mitochondrial perturbations and laying a foundation for mechanistic investigations into protein function. Guided by these data, we discovered that PIGY upstream open reading frame (PYURF) is an S-adenosylmethionine-dependent methyltransferase chaperone that supports both complex I assembly and coenzyme Q biosynthesis and is disrupted in a previously unresolved multisystemic mitochondrial disorder. We further linked the putative zinc transporter SLC30A9 to mitochondrial ribosomes and OxPhos integrity and established RAB5IF as the second gene harbouring pathogenic variants that cause cerebrofaciothoracic dysplasia. Our data, which can be explored through the interactive online MITOMICS.app resource, suggest biological roles for many other orphan mitochondrial proteins that still lack robust functional characterization and define a rich cell signature of mitochondrial dysfunction that can support the genetic diagnosis of mitochondrial diseases.

DOI: https://doi.org/10.1038/s41586-022-04765-3
MicroPubl Biol. 2022 ;2022

Genetic screen identifies non-mitochondrial proteins involved in the maintenance of mitochondrial homeostasis.

Stephane Rolland, Barbara Conradt.

The mitochondrial unfolded protein response (UPR mt ) is an important stress response that ensures the maintenance of mitochondrial homeostasis in response to various types of cellular stress. We previously described a genetic screen for Caenorhabditis elegans genes, which when inactivated cause UPR mt activation, and reported genes identified that encode mitochondrial proteins. We now report additional genes identified in the screen. Importantly, these include genes that encode non-mitochondrial proteins involved in processes such as the control of gene expression, post-translational modifications, cell signaling and cellular trafficking. Interestingly, we identified several genes that have been proposed to participate in the transfer of lipids between peroxisomes, ER and mitochondria, suggesting that lipid transfer between these organelles is essential for mitochondrial homeostasis. In conclusion, this study shows that the maintenance of mitochondrial homeostasis is not only dependent on mitochondrial processes but also relies on non-mitochondrial processes and pathways. Our results reinforce the notion that mitochondrial function and cellular function are intimately connected.

DOI: https://doi.org/10.17912/micropub.biology.000562
Aging Cell. 2022 May 22. e13622

Defective mitophagy in aged macrophages promotes mitochondrial DNA cytosolic leakage to activate STING signaling during liver sterile inflammation.

Weizhe Zhong, Zhuqing Rao, Jian Xu, Yu Sun, Haoran Hu, Ping Wang, Yongxiang Xia, Xiongxiong Pan, Weiwei Tang, Ziyi Chen, Haoming Zhou, Xuehao Wang.

  Macrophage-stimulator of interferon genes (STING) signaling mediated sterile inflammation has been implicated in various age-related diseases. However, whether and how macrophage mitochondrial DNA (mtDNA) regulates STING signaling in aged macrophages remains largely unknown. We found that hypoxia-reoxygenation (HR) induced STING activation in macrophages by triggering the release of macrophage mtDNA into the cytosol. Aging promoted the cytosolic leakage of macrophage mtDNA and enhanced STING activation, which was abrogated upon mtDNA depletion or cyclic GMP-AMP Synthase (cGAS) inhibition. Aged macrophages exhibited increased mitochondrial injury with impaired mitophagy. Mechanistically, a decline in the PTEN-induced kinase 1 (PINK1)/Parkin-mediated polyubiquitination of mitochondria was observed in aged macrophages. Pink1 overexpression reversed the inhibition of mitochondrial ubiquitination but failed to promote mitolysosome formation in the aged macrophages. Meanwhile, aging impaired lysosomal biogenesis and function in macrophages by modulating the mTOR/transcription factor EB (TFEB) signaling pathway, which could be reversed by Torin-1 treatment. Consequently, Pink1 overexpression in combination with Torin-1 treatment restored mitophagic flux and inhibited mtDNA/cGAS/STING activation in aged macrophages. Moreover, besides HR-induced metabolic stress, other types of oxidative and hepatotoxic stresses inhibited mitophagy and promoted the cytosolic release of mtDNA to activate STING signaling in aged macrophages. STING deficiency protected aged mice against diverse types of sterile inflammatory liver injuries. Our findings suggest that aging impairs mitophagic flux to facilitate the leakage of macrophage mtDNA into the cytosol and promotes STING activation, and thereby provides a novel potential therapeutic target for sterile inflammatory liver injury in aged patients.

Keywords:  aging; macrophage; mitochondrial DNA; mitophagy; sterile inflammation; stimulator of interferon genes

DOI:  https://doi.org/10.1111/acel.13622
Heliyon. 2022 May;8(5): e09353

Mitochondrial respiratory chain protein co-regulation in the human brain.

Caroline Trumpff, Edward Owusu-Ansah, Hans-Ulrich Klein, Annie J Lee, Vladislav Petyuk, Thomas S Wingo, Aliza P Wingo, Madhav Thambisetty, Luigi Ferrucci, Nicholas T Seyfried, David A Bennett, Philip L De Jager, Martin Picard.

  Mitochondrial respiratory chain (RC) function requires the stoichiometric interaction among dozens of proteins but their co-regulation has not been defined in the human brain. Here, using quantitative proteomics across three independent cohorts we systematically characterized the co-regulation patterns of mitochondrial RC proteins in the human dorsolateral prefrontal cortex (DLPFC). Whereas the abundance of RC protein subunits that physically assemble into stable complexes were correlated, indicating their co-regulation, RC assembly factors exhibited modest co-regulation. Within complex I, nuclear DNA-encoded subunits exhibited >2.5-times higher co-regulation than mitochondrial (mt)DNA-encoded subunits. Moreover, mtDNA copy number was unrelated to mtDNA-encoded subunits abundance, suggesting that mtDNA content is not limiting. Alzheimer's disease (AD) brains exhibited reduced abundance of complex I RC subunits, an effect largely driven by a 2-4% overall lower mitochondrial protein content. These findings provide foundational knowledge to identify molecular mechanisms contributing to age- and disease-related erosion of mitochondrial function in the human brain.

Keywords:  Alzheimer disease; BLSA; Banner; Mitochondrial respiratory chain; Post-mortem brain; Proteomics; ROSMAP

DOI:  https://doi.org/10.1016/j.heliyon.2022.e09353
J Cell Biochem. 2022 May 26.

Disruption of the MICOS complex leads to an aberrant cristae structure and an unexpected, pronounced lifespan extension in Podospora anserina.

Verena Warnsmann, Lisa-Marie Marschall, Anja C Meeßen, Maike Wolters, Lea Schürmanns, Marion Basoglu, Stefan Eimer, Heinz D Osiewacz.

  Mitochondria are dynamic eukaryotic organelles involved in a variety of essential cellular processes including the generation of adenosine triphosphate (ATP) and reactive oxygen species as well as in the control of apoptosis and autophagy. Impairments of mitochondrial functions lead to aging and disease. Previous work with the ascomycete Podospora anserina demonstrated that mitochondrial morphotype as well as mitochondrial ultrastructure change during aging. The latter goes along with an age-dependent reorganization of the inner mitochondrial membrane leading to a change from lamellar cristae to vesicular structures. Particularly from studies with yeast, it is known that besides the F1 Fo -ATP-synthase and the phospholipid cardiolipin also the "mitochondrial contact site and cristae organizing system" (MICOS) complex, existing of the Mic60- and Mic10-subcomplex, is essential for proper cristae formation. In the present study, we aimed to understand the mechanistic basis of age-related changes in the mitochondrial ultrastructure. We observed that MICOS subunits are coregulated at the posttranscriptional level. This regulation partially depends on the mitochondrial iAAA-protease PaIAP. Most surprisingly, we made the counterintuitive observation that, despite the loss of lamellar cristae and of mitochondrial impairments, the ablation of MICOS subunits (except for PaMIC12) leads to a pronounced lifespan extension. Moreover, simultaneous ablation of subunits of both MICOS subcomplexes synergistically increases lifespan, providing formal genetic evidence that both subcomplexes affect lifespan by different and at least partially independent pathways. At the molecular level, we found that ablation of Mic10-subcomplex components leads to a mitohormesis-induced lifespan extension, while lifespan extension of Mic60-subcomplex mutants seems to be controlled by pathways involved in the control of phospholipid homeostasis. Overall, our data demonstrate that both MICOS subcomplexes have different functions and play distinct roles in the aging process of P. anserina.

Keywords:  MICOS; Podospora anserina; aging; cristae; mitochondria; mitohormesis

DOI:  https://doi.org/10.1002/jcb.30278
J Cell Biol. 2022 Jul 04. pii: e202201071. [Epub ahead of print]221(7):

The UPRmt preserves mitochondrial import to extend lifespan.

Nan Xin, Jenni Durieux, Chunxia Yang, Suzanne Wolff, Hyun-Eui Kim, Andrew Dillin.

The mitochondrial unfolded protein response (UPRmt) is dedicated to promoting mitochondrial proteostasis and is linked to extreme longevity. The key regulator of this process is the transcription factor ATFS-1, which, upon UPRmt activation, is excluded from the mitochondria and enters the nucleus to regulate UPRmt genes. However, the repair proteins synthesized as a direct result of UPRmt activation must be transported into damaged mitochondria that had previously excluded ATFS-1 owing to reduced import efficiency. To address this conundrum, we analyzed the role of the import machinery when the UPRmt was induced. Using in vitro and in vivo analysis of mitochondrial proteins, we surprisingly find that mitochondrial import increases when the UPRmt is activated in an ATFS-1-dependent manner, despite reduced mitochondrial membrane potential. The import machinery is upregulated, and an intact import machinery is essential for UPRmt-mediated lifespan extension. ATFS-1 has a weak mitochondrial targeting sequence (MTS), allowing for dynamic subcellular localization during the initial stages of UPRmt activation.

DOI: https://doi.org/10.1083/jcb.202201071
Redox Biol. 2022 May 13. pii: S2213-2317(22)00107-0. [Epub ahead of print]53 102335

Mitochondrial thioredoxin system is required for enhanced stress resistance and extended longevity in long-lived mitochondrial mutants.

Namastheé Harris-Gauthier, Annika Traa, Abdelrahman AlOkda, Alibek Moldakozhayev, Ulrich Anglas, Sonja K Soo, Jeremy M Van Raamsdonk.

  Mild impairment of mitochondrial function has been shown to increase lifespan in genetic model organisms including worms, flies and mice. To better understand the mechanisms involved, we analyzed RNA sequencing data and found that genes involved in the mitochondrial thioredoxin system, trx-2 and trxr-2, are specifically upregulated in long-lived mitochondrial mutants but not other non-mitochondrial, long-lived mutants. Upregulation of trx-2 and trxr-2 is mediated by activation of the mitochondrial unfolded protein response (mitoUPR). While we decided to focus on the genes of the mitochondrial thioredoxin system for this paper, we identified multiple other antioxidant genes that are upregulated by the mitoUPR in the long-lived mitochondrial mutants including sod-3, prdx-3, gpx-6, gpx-7, gpx-8 and glrx-5. In exploring the role of the mitochondrial thioredoxin system in the long-lived mitochondrial mutants, nuo-6 and isp-1, we found that disruption of either trx-2 or trxr-2 significantly decreases their long lifespan, but has no effect on wild-type lifespan, indicating that the mitochondrial thioredoxin system is specifically required for their longevity. In contrast, disruption of the cytoplasmic thioredoxin gene trx-1 decreases lifespan in nuo-6, isp-1 and wild-type worms, indicating a non-specific detrimental effect on longevity. Disruption of trx-2 or trxr-2 also decreases the enhanced resistance to stress in nuo-6 and isp-1 worms, indicating a role for the mitochondrial thioredoxin system in protecting against exogenous stressors. Overall, this work demonstrates an important role for the mitochondrial thioredoxin system in both stress resistance and lifespan resulting from mild impairment of mitochondrial function.

Keywords:  Aging; Antioxidant; C. elegans; Mitochondria; Reactive oxygen species; Thioredoxin

DOI:  https://doi.org/10.1016/j.redox.2022.102335
Mitochondrion. 2022 May 24. pii: S1567-7249(22)00048-4. [Epub ahead of print]

Triplication of HSA21 on alterations in structure and function of mitochondria.

Bani Bandana Ganguly, Nitin N Kadam.

  Triplication of genes encoded in human chromosome 21 (HSA21) is responsible for the phenotypes of Down syndrome (DS). The dosage-imbalance of the nuclear genes and the extra-nuclear mitochondrial DNA (mtDNA) jointly contributes to patho-mechanisms in DS. The mitochondrial organelles are the power house of cells for generation of ATP and maintaining cellular calcium and redox homeostasis, and cellular energy-metabolism processes. Each cell contains hundreds to thousands of mitochondria depending on their energy consumption. The dynamic structure of mitochondria is maintained with continuous fission and fusion events, and thus, content of mtDNA and its genetic composition are widely variable among cells. Cells of brain and heart tissues of DS patients and DS-mouse models have demonstrated elevated number but reduced amount of mtDNA due to higher fission process. This mechanism perturbs the oxidative phosphorylation (OXPHOS) and generates more free radicals such as reactive oxygen species (ROS), suggesting contribution of mtDNA in proliferation and protection of cells from endogenous toxic environment and external stressors. Gene-dosage in DS population collectively contributes to mitochondrial dysfunction by lowering energy production and respiratory capacity via the impaired OXPHOS, and damaged redox homeostasis and mitochondrial dynamics in all types of cells in DS. The context is highly complex and affects the functioning of all organs. The effect in brain and heart tissues promotes myriads of neurodegenerative diseases and cardiac complexities in individuals with DS. Crosstalk between trisomic nuclear and mitochondrial genome has been crucial for identification of potential therapeutic targets.

Keywords:  Down syndrome; bioenergetics and biogenesis of mitochondria; mitochondrial dynamics; mitochondrial dysfunction and oxidative stress; mitophagy

DOI:  https://doi.org/10.1016/j.mito.2022.05.007
Mitochondrion. 2022 May 24. pii: S1567-7249(22)00045-9. [Epub ahead of print]

A new hope: Mitochondria, a critical factor in the war against prions.

Kevin Zambrano, Diego Barba, Karina Castillo, Paola Robayo, Eduardo Arizaga, Andrés Caicedo, Antonio W D Gavilanes.

  Prion diseases encompass a group of incurable neurodegenerative disorders that occur due to the misfolding and aggregation of infectious proteins. The most well-known prion diseases are Creutzfeldt-Jakob disease (CJD), bovine spongiform encephalopathy (also known as mad cow disease), and kuru. It is estimated that around 1-2 persons per million worldwide are affected annually by prion disorders. Infectious prion proteins propagate in the brain, clustering in the cells and rapidly inducing tissue degeneration and death. Prion disease alters cell metabolism and energy production damaging mitochondrial function and dynamics leading to a fast accumulation of damage. Dysfunction of mitochondria could be considered as an early precursor and central element in the pathogenesis of prion diseases such as in sporadic CJD. Preserving mitochondria function may help to resist the rapid spread and damage of prion proteins and even clearance. In the war against prions and other degenerative diseases, studying how to preserve the function of mitochondria by using antioxidants and even replacing them with artificial mitochondrial transfer/transplant (AMT/T) may bring a new hope and lead to an increase in patients' survival. In this perspective review, we provide key insights about the relationship between the progression of prion disease and mitochondria, in which understanding how protecting mitochondria function and viability by using antioxidants or AMT/T may help to develop novel therapeutic interventions.

Keywords:  extracellular mitochondria; mitochondrial therapy; mtDNA; neurodegenerative disease; prions

DOI:  https://doi.org/10.1016/j.mito.2022.05.004
Cell Death Differ. 2022 May 25.

The mitochondrial chaperone TRAP1 regulates F-ATP synthase channel formation.

Giuseppe Cannino, Andrea Urbani, Marco Gaspari, Mariaconcetta Varano, Alessandro Negro, Antonio Filippi, Francesco Ciscato, Ionica Masgras, Christoph Gerle, Elena Tibaldi, Anna Maria Brunati, Giorgio Colombo, Giovanna Lippe, Paolo Bernardi, Andrea Rasola.

Binding of the mitochondrial chaperone TRAP1 to client proteins shapes bioenergetic and proteostatic adaptations of cells, but the panel of TRAP1 clients is only partially defined. Here we show that TRAP1 interacts with F-ATP synthase, the protein complex that provides most cellular ATP. TRAP1 competes with the peptidyl-prolyl cis-trans isomerase cyclophilin D (CyPD) for binding to the oligomycin sensitivity-conferring protein (OSCP) subunit of F-ATP synthase, increasing its catalytic activity and counteracting the inhibitory effect of CyPD. Electrophysiological measurements indicate that TRAP1 directly inhibits a channel activity of purified F-ATP synthase endowed with the features of the permeability transition pore (PTP) and that it reverses PTP induction by CyPD, antagonizing PTP-dependent mitochondrial depolarization and cell death. Conversely, CyPD outcompetes the TRAP1 inhibitory effect on the channel. Our data identify TRAP1 as an F-ATP synthase regulator that can influence cell bioenergetics and survival and can be targeted in pathological conditions where these processes are dysregulated, such as cancer.

DOI: https://doi.org/10.1038/s41418-022-01020-0
Genes Dev. 2022 May 26.

Senescence-induced endothelial phenotypes underpin immune-mediated senescence surveillance.

Kelvin Yin, Daniel Patten, Sarah Gough, Susana de Barros Gonçalves, Adelyne Chan, Ioana Olan, Liam Cassidy, Marta Poblocka, Haoran Zhu, Aaron Lun, Martijn Schuijs, Andrew Young, Celia Martinez-Jimenez, Timotheus Y F Halim, Shishir Shetty, Masashi Narita, Matthew Hoare.

  Senescence is a stress-responsive tumor suppressor mechanism associated with expression of the senescence-associated secretory phenotype (SASP). Through the SASP, senescent cells trigger their own immune-mediated elimination, which if evaded leads to tumorigenesis. Senescent parenchymal cells are separated from circulating immunocytes by the endothelium, which is targeted by microenvironmental signaling. Here we show that SASP induces endothelial cell NF-κB activity and that SASP-induced endothelial expression of the canonical NF-κB component Rela underpins senescence surveillance. Using human liver sinusoidal endothelial cells (LSECs), we show that SASP-induced endothelial NF-κB activity regulates a conserved transcriptional program supporting immunocyte recruitment. Furthermore, oncogenic hepatocyte senescence drives murine LSEC NF-κB activity in vivo. Critically, we show two distinct endothelial pathways in senescence surveillance. First, endothelial-specific loss of Rela prevents development of Stat1-expressing CD4+ T lymphocytes. Second, the SASP up-regulates ICOSLG on LSECs, with the ICOS-ICOSLG axis contributing to senescence cell clearance. Our results show that the endothelium is a nonautonomous SASP target and an organizing center for immune-mediated senescence surveillance.

Keywords:  NF-κB; SASP; endothelium; immune surveillance; liver; senescence

DOI:  https://doi.org/10.1101/gad.349585.122
EMBO Rep. 2022 May 25. e55423

Money, power, and mitochondria.

Howy Jacobs.

Can we devise ways for the ultra-rich to put their wealth to good use?

DOI: https://doi.org/10.15252/embr.202255423
Trends Cell Biol. 2022 May 20. pii: S0962-8924(22)00116-7. [Epub ahead of print]

The heterogeneity of cellular senescence: insights at the single-cell level.

Rachel L Cohn, Nathan S Gasek, George A Kuchel, Ming Xu.

  Senescent cells are highly associated with aging and pathological conditions and could be targeted to slow the aging process. One commonly used marker to examine senescent cells in vivo is p16, which has led to important discoveries. Recent studies have also described new senescence markers beyond p16 and have highlighted the importance of investigating senescence heterogeneity in cell types and tissues. With the development of high-throughput technologies, such as single-cell RNA-seq and single-nucleus RNA-seq, we can examine senescent cells at the single-cell level and potentially uncover new markers. This review emphasizes that there is an urgent need to investigate senescence heterogeneity and discuss how this could be accomplished by using advanced technologies and sequencing datasets.

Keywords:  RNA-sequencing; aging; p16; p21; senolytics

DOI:  https://doi.org/10.1016/j.tcb.2022.04.011
Biomol Concepts. 2022 May 26. 13(1): 272-288

Supercomplex supercomplexes: Raison d'etre and functional significance of supramolecular organization in oxidative phosphorylation.

Sunil Nath.

  Following structural determination by recent advances in electron cryomicroscopy, it is now well established that the respiratory Complexes I-IV in oxidative phosphorylation (OXPHOS) are organized into supercomplexes in the respirasome. Nonetheless, the reason for the existence of the OXPHOS supercomplexes and their functional role remains an enigma. Several hypotheses have been proposed for the existence of these supercomplex supercomplexes. A commonly-held view asserts that they enhance catalysis by substrate channeling. However, this - and other views - has been challenged based on structural and biophysical information. Hence, new ideas, concepts, and frameworks are needed. Here, a new model of energy transfer in OXPHOS is developed on the basis of biochemical data on the pure competitive inhibition of anionic substrates like succinate by the classical anionic uncouplers of OXPHOS (2,4-dinitrophenol, carbonyl cyanide 4-(trifluoromethoxy)phenylhydrazone, and dicoumarol), and pharmacological data on the unique site-selective, energy-linked inhibition of energy conservation pathways in mitochondria induced by the guanidine derivatives. It is further found that uncouplers themselves are site-specific and exhibit differential selectivity and efficacy in reversing the inhibition caused by the Site 1/Complex I or Site 2/Complexes II-III-selective guanidine derivatives. These results lead to new vistas and sufficient complexity in the network of energy conservation pathways in the mitochondrial respiratory chain that necessitate discrete points of interaction with two classes of guanidine derivatives and uncoupling agents and thereby separate and distinct energy transfer pathways between Site 1 and Site 2 and the intermediate that energizes adenosine triphosphate (ATP) synthesis by Complex V. Interpretation based on Mitchell's single-ion chemiosmotic theory that postulates only a single energy pool is inadequate to rationalize the data and account for the required complexity. The above results and available information are shown to be explained by Nath's two-ion theory of energy coupling and ATP synthesis, involving coupled movement of succinate anions and protons, along with the requirement postulated by the theory for maintenance of homeostasis and ion translocation across the energy-transducing membrane of both succinate monoanions and succinate dianions by Complexes I-V in the OXPHOS supercomplexes. The new model of energy transfer in mitochondria is mapped onto the solved structures of the supercomplexes and integrated into a consistent model with the three-dimensional electron microscope computer tomography visualization of the internal structure of the cristae membranes in mammalian mitochondria. The model also offers valuable insights into diseased states induced in type 2 diabetes and especially in Alzheimer's and other neurodegenerative diseases that involve mitochondrial dysfunction.

Keywords:  2,4-dinitrophenol; Alzheimer’s disease; Complexes I–V; Gunnar Hollunger’s pioneering work in pharmacology; Mitchell’s single-ion chemiosmotic theory; Nath’s torsional mechanism of energy transduction and ATP synthesis; Nath’s two-ion theory of energy coupling; OXPHOS supercomplexes; Paolo Bernardi’s pioneering work on cell death and ATP; alkylguanidines; carbonyl cyanide 4-(trifluoromethoxy)phenylhydrazone; competitive inhibition of succinate with the anionic uncouplers of OXPHOS; coupling of proton and succinate anion transport; dicoumarol; differential release of inhibition by pharmacological agents by uncouplers; functional role of the OXPHOS supercomplexes; inhibition of succinate entry by uncouplers; integrated mitochondrial function; interaction of site-specific guanidine derivatives with mitochondria; mitochondrial dysfunction; new definition of mitochondrial respiration; new model of energy transfer in mitochondria; octylguanidines; oxidative phosphorylation; phenethylbiguanides; sensing of local electrical potential, Δψ; supramolecular biology; supramolecular chemistry; translocation of succinate monoanions and succinate dianions across cristae membranes; two distinct energy conservation pathways between the electron transport chain and FOF1-ATP synthase; type 2 diabetes

DOI:  https://doi.org/10.1515/bmc-2022-0021