bims-mimbat 2023-04-02 papers

bims-mimbat

Biomed News

on Mitochondrial metabolism in brown adipose tissue

Issue of 2023–04–02
thirteen papers selected by
José Carlos de Lima-Júnior, Washington University

Cristae formation is a mechanical buckling event controlled by the inner membrane lipidome.
Age-dependent Pdgfrβ signaling drives adipocyte progenitor dysfunction to alter the beige adipogenic niche in male mice.
Aging impairs cold-induced beige adipogenesis and adipocyte metabolic reprogramming.
PRL-1/2 phosphatases control TRPM7 magnesium-dependent function to regulate cellular bioenergetics.
Mitochondria Need Their Sleep: Redox, Bioenergetics, and Temperature Regulation of Circadian Rhythms and the Role of Cysteine-Mediated Redox Signaling, Uncoupling Proteins, and Substrate Cycles.
Temporal inhibition of the electron transport chain attenuates stress-induced cellular senescence by prolonged disturbance of proteostasis in human fibroblasts.
Molecular mechanism on forcible ejection of ATPase inhibitory factor 1 from mitochondrial ATP synthase.
Substrate recognition and proton coupling by a bacterial member of solute carrier family 17.
Hem25p is a mitochondrial IPP transporter.
Evolution: 'Millefoglie' origin of mitochondrial cristae.
Cytosolic and mitochondrial NADPH fluxes are independently regulated.
SUCNR1 signaling in adipocytes controls energy metabolism by modulating circadian clock and leptin expression.
Membrane phospholipid remodeling modulates nonalcoholic steatohepatitis progression by regulating mitochondrial homeostasis.

bioRxiv. 2023 Mar 15. pii: 2023.03.13.532310. [Epub ahead of print]

Cristae formation is a mechanical buckling event controlled by the inner membrane lipidome.

Kailash Venkatraman, Christopher T Lee, Guadalupe C Garcia, Arijit Mahapatra, Guy Perkins, Keun-Young Kim, Hilda Amalia Pasolli, Sebastien Phan, Jennifer Lippincott-Schwartz, Mark Ellisman, Padmini Rangamani, Itay Budin.

The inner mitochondrial membrane (IMM) is the site of bulk ATP generation in cells and has a broadly conserved lipid composition enriched in unsaturated phospholipids and cardiolipin (CL). While proteins that shape the IMM and its characteristic cristae membranes (CM) have been defined, specific mechanisms by which mitochondrial lipids dictate its structure and function have yet to be elucidated. Here we combine experimental lipidome dissection with multi-scale modeling to investigate how lipid interactions shape CM morphology and ATP generation. When modulating fatty acid unsaturation in engineered yeast strains, we observed that loss of di-unsaturated phospholipids (PLs) led to a breakpoint in IMM topology and respiratory capacity. We found that PL unsaturation modulates the organization of ATP synthases that shape cristae ridges. Based on molecular modeling of mitochondrial-specific membrane adaptations, we hypothesized that conical lipids like CL buffer against the effects of saturation on the IMM. In cells, we discovered that loss of CL collapses the IMM at intermediate levels of PL saturation, an effect that is independent of ATP synthase oligomerization. To explain this interaction, we employed a continuum modeling approach, finding that lipid and protein-mediated curvatures are predicted to act in concert to form curved membranes in the IMM. The model highlighted a snapthrough instability in cristae tubule formation, which could drive IMM collapse upon small changes in composition. The interaction between CL and di-unsaturated PLs suggests that growth conditions that alter the fatty acid pool, such as oxygen availability, could define CL function. While loss of CL only has a minimal phenotype under standard laboratory conditions, we show that its synthesis is essential under microaerobic conditions that better mimic natural yeast fermentation. Lipid and protein-mediated mechanisms of curvature generation can thus act together to support mitochondrial architecture under changing environments.

DOI: https://doi.org/10.1101/2023.03.13.532310
Nat Commun. 2023 Mar 31. 14(1): 1806

Age-dependent Pdgfrβ signaling drives adipocyte progenitor dysfunction to alter the beige adipogenic niche in male mice.

Abigail M Benvie, Derek Lee, Benjamin M Steiner, Siwen Xue, Yuwei Jiang, Daniel C Berry.

Perivascular adipocyte progenitor cells (APCs) can generate cold temperature-induced thermogenic beige adipocytes within white adipose tissue (WAT), an effect that could counteract excess fat mass and metabolic pathologies. Yet, the ability to generate beige adipocytes declines with age, creating a key challenge for their therapeutic potential. Here we show that ageing beige APCs overexpress platelet derived growth factor receptor beta (Pdgfrβ) to prevent beige adipogenesis. We show that genetically deleting Pdgfrβ, in adult male mice, restores beige adipocyte generation whereas activating Pdgfrβ in juvenile mice blocks beige fat formation. Mechanistically, we find that Stat1 phosphorylation mediates Pdgfrβ beige APC signaling to suppress IL-33 induction, which dampens immunological genes such as IL-13 and IL-5. Moreover, pharmacologically targeting Pdgfrβ signaling restores beige adipocyte development by rejuvenating the immunological niche. Thus, targeting Pdgfrβ signaling could be a strategy to restore WAT immune cell function to stimulate beige fat in adult mammals.

DOI: https://doi.org/10.1038/s41467-023-37386-z
bioRxiv. 2023 Mar 23. pii: 2023.03.20.533514. [Epub ahead of print]

Aging impairs cold-induced beige adipogenesis and adipocyte metabolic reprogramming.

Corey D Holman, Alexander P Sakers, Ryan P Calhoun, Lan Cheng, Ethan C Fein, Christopher Jacobs, Linus Tsai, Evan D Rosen, Patrick Seale.

The energy-burning capability of beige adipose tissue is a potential therapeutic tool for reducing obesity and metabolic disease, but this capacity is decreased by aging. Here, we evaluate the impact of aging on the profile and activity of adipocyte stem and progenitor cells (ASPCs) and adipocytes during the beiging process. We found that aging increases the expression of Cd9 and other fibrogenic genes in fibroblastic ASPCs and blocks their differentiation into beige adipocytes. Fibroblastic ASPC populations from young and aged mice were equally competent for beige differentiation in vitro , suggesting that environmental factors suppress adipogenesis in vivo . Examination of adipocytes by single nucleus RNA-sequencing identified compositional and transcriptional differences in adipocyte populations with age and cold exposure. Notably, cold exposure induced an adipocyte population expressing high levels of de novo lipogenesis (DNL) genes, and this response was severely blunted in aged animals. We further identified natriuretic peptide clearance receptor Npr3 , a beige fat repressor, as a marker gene for a subset of white adipocytes and an aging-upregulated gene in adipocytes. In summary, this study indicates that aging blocks beige adipogenesis and dysregulates adipocyte responses to cold exposure and provides a unique resource for identifying cold and/or aging-regulated pathways in adipose tissue.

DOI: https://doi.org/10.1101/2023.03.20.533514
Proc Natl Acad Sci U S A. 2023 Apr 04. 120(14): e2221083120

PRL-1/2 phosphatases control TRPM7 magnesium-dependent function to regulate cellular bioenergetics.

Serge Hardy, Yevgen Zolotarov, Jacob Coleman, Simon Roitman, Hira Khursheed, Isabelle Aubry, Noriko Uetani, Michel L Tremblay.

  Phosphatases of regenerating liver (PRL-1, PRL-2, PRL-3; also known as PTP4A1, PTP4A2, PTP4A3, respectively) control intracellular magnesium levels by interacting with the CNNM magnesium transport regulators. Still, the exact mechanism governing magnesium transport by this protein complex is not well understood. Herein, we have developed a genetically encoded intracellular magnesium-specific reporter and demonstrate that the CNNM family inhibits the function of the TRPM7 magnesium channel. We show that the small GTPase ARL15 increases CNNM3/TRPM7 protein complex formation to reduce TRPM7 activity. Conversely, PRL-2 overexpression counteracts ARL15 binding to CNNM3 and enhances the function of TRPM7 by preventing the interaction between CNNM3 and TRPM7. Moreover, while TRPM7-induced cell signaling is promoted by PRL-1/2, it is reduced when CNNM3 is overexpressed. Lowering cellular magnesium levels reduces the interaction of CNNM3 with TRPM7 in a PRL-dependent manner, whereby knockdown of PRL-1/2 restores the protein complex formation. Cotargeting of TRPM7 and PRL-1/2 alters mitochondrial function and sensitizes cells to metabolic stress induced by magnesium depletion. These findings reveal the dynamic regulation of TRPM7 function in response to PRL-1/2 levels, to coordinate magnesium transport and reprogram cellular metabolism.

Keywords:  PRL phosphatase; TRPM7; magnesium; magnesium sensor; metabolism

DOI:  https://doi.org/10.1073/pnas.2221083120
Antioxidants (Basel). 2023 Mar 09. pii: 674. [Epub ahead of print]12(3):

Mitochondria Need Their Sleep: Redox, Bioenergetics, and Temperature Regulation of Circadian Rhythms and the Role of Cysteine-Mediated Redox Signaling, Uncoupling Proteins, and Substrate Cycles.

Richard B Richardson, Ryan J Mailloux.

  Although circadian biorhythms of mitochondria and cells are highly conserved and crucial for the well-being of complex animals, there is a paucity of studies on the reciprocal interactions between oxidative stress, redox modifications, metabolism, thermoregulation, and other major oscillatory physiological processes. To address this limitation, we hypothesize that circadian/ultradian interaction of the redoxome, bioenergetics, and temperature signaling strongly determine the differential activities of the sleep-wake cycling of mammalians and birds. Posttranslational modifications of proteins by reversible cysteine oxoforms, S-glutathionylation and S-nitrosylation are shown to play a major role in regulating mitochondrial reactive oxygen species production, protein activity, respiration, and metabolomics. Nuclear DNA repair and cellular protein synthesis are maximized during the wake phase, whereas the redoxome is restored and mitochondrial remodeling is maximized during sleep. Hence, our analysis reveals that wakefulness is more protective and restorative to the nucleus (nucleorestorative), whereas sleep is more protective and restorative to mitochondria (mitorestorative). The "redox-bioenergetics-temperature and differential mitochondrial-nuclear regulatory hypothesis" adds to the understanding of mitochondrial respiratory uncoupling, substrate cycling control and hibernation. Similarly, this hypothesis explains how the oscillatory redox-bioenergetics-temperature-regulated sleep-wake states, when perturbed by mitochondrial interactome disturbances, influence the pathogenesis of aging, cancer, spaceflight health effects, sudden infant death syndrome, and diseases of the metabolism and nervous system.

Keywords:  bioenergetics; circadian; cysteine oxoforms; mitochondria; nuclear; oxidative stress; redoxome; substrate cycles; temperature; uncoupling

DOI:  https://doi.org/10.3390/antiox12030674
FEBS J. 2023 Apr 01.

Temporal inhibition of the electron transport chain attenuates stress-induced cellular senescence by prolonged disturbance of proteostasis in human fibroblasts.

Yasuhiro Takenaka, Ikuo Inoue, Masataka Hirasaki, Masaaki Ikeda, Yoshihiko Kakinuma.

  We previously developed a stress-induced premature senescence (SIPS) model in which normal human fibroblast MRC-5 cells were treated with either the proteasome inhibitor MG132 or the vacuolar-type ATPase (V-ATPase) inhibitor bafilomycin A1 (BAFA1). To clarify the involvement of mitochondrial function in our SIPS model, MRC-5 cells were treated with MG132 or BAFA1 along with an inhibitor targeting either the electron transport chain (ETC) complex I or complex III, or with a mitochondrial uncoupler. SIPS induced by MG132 or BAFA1 was significantly attenuated by short-term co-treatment with the complex III inhibitor, antimycin A (AA), but not the complex I inhibitor, rotenone, or the mitochondrial uncoupler, carbonyl cyanide 3-chlorophenylhydrazone (CCCP). By co-treatment with AA, mitochondrial and intracellular reactive oxygen species (ROS) levels, accumulation of protein aggregates, and mitochondrial unfolded protein responses (UPRmt ) were remarkably suppressed. Furthermore, AA co-treatment suppressed the hyperpolarization of the mitochondrial membrane and the induction of mitophagy observed in MG132-treated cells, and enhanced mitochondrial biogenesis. These findings provide evidence that the temporal inhibition of mitochondrial respiration exerts protective effects against the progression of premature senescence caused by impaired proteostasis.

Keywords:  MG132; mitochondria; oxidative phosphorylation; proteostasis; senescence; unfolded protein response

DOI:  https://doi.org/10.1111/febs.16785
Nat Commun. 2023 Mar 31. 14(1): 1682

Molecular mechanism on forcible ejection of ATPase inhibitory factor 1 from mitochondrial ATP synthase.

Ryohei Kobayashi, Hiroshi Ueno, Kei-Ichi Okazaki, Hiroyuki Noji.

IF1 is a natural inhibitor protein for mitochondrial FoF1 ATP synthase that blocks catalysis and rotation of the F1 by deeply inserting its N-terminal helices into F1. A unique feature of IF1 is condition-dependent inhibition; although IF1 inhibits ATP hydrolysis by F1, IF1 inhibition is relieved under ATP synthesis conditions. To elucidate this condition-dependent inhibition mechanism, we have performed single-molecule manipulation experiments on IF1-inhibited bovine mitochondrial F1 (bMF1). The results show that IF1-inhibited F1 is efficiently activated only when F1 is rotated in the clockwise (ATP synthesis) direction, but not in the counterclockwise direction. The observed rotational-direction-dependent activation explains the condition-dependent mechanism of IF1 inhibition. Investigation of mutant IF1 with N-terminal truncations shows that the interaction with the γ subunit at the N-terminal regions is crucial for rotational-direction-dependent ejection, and the middle long helix is responsible for the inhibition of F1.

DOI: https://doi.org/10.1038/s41467-023-37182-9
J Biol Chem. 2023 Mar 23. pii: S0021-9258(23)00288-0. [Epub ahead of print] 104646

Substrate recognition and proton coupling by a bacterial member of solute carrier family 17.

Samir Batarni, Nanda Nayak, Audrey Chang, Fei Li, Surabhi Hareendranath, Lexi Zhou, Hongfei Xu, Robert Stroud, Jacob Eriksen, Robert H Edwards.

  The solute carrier 17 (SLC17) family transports diverse organic anions using two distinct modes of coupling to a source of energy. Transporters that package glutamate and nucleotide into secretory vesicles for regulated release by exocytosis are driven by membrane potential but subject to allosteric regulation by H+ and Cl-. Other SLC17 members including the lysosomal sialic acid exporter couple the flux of organic anion to cotransport of H+. To begin to understand how similar proteins can perform such different functions, we have studied E. coli DgoT, a H+/galactonate cotransporter. A recent structure of DgoT showed many residues contacting D-galactonate, and we now find that they do not tolerate even conservative substitutions. In contrast, the closely related lysosomal H+/sialic acid cotransporter Sialin tolerates similar mutations, consistent with its recognition of diverse substrates with relatively low affinity. We also find that despite coupling to H+, DgoT transports more rapidly but with lower apparent affinity at high pH. Indeed, membrane potential can drive uptake, indicating electrogenic transport and suggesting a H+ : galactonate stoichiometry >1. Located in a polar pocket of the N-terminal helical bundle, Asp46 and Glu133 are each required for net flux by DgoT, but the E133Q mutant exhibits robust exchange activity and rescues exchange by D46N, suggesting that these two residues operate in series to translocate protons. E133Q also shifts the pH sensitivity of exchange by DgoT, supporting a central role for the highly conserved TM4 glutamate in H+ coupling by DgoT.

Keywords:  anion transport; proton motive force; proton transport; transporter

DOI:  https://doi.org/10.1016/j.jbc.2023.104646
bioRxiv. 2023 Mar 14. pii: 2023.03.14.532620. [Epub ahead of print]

Hem25p is a mitochondrial IPP transporter.

Jonathan Tai, Rachel M Guerra, Sean W Rogers, Zixiang Fang, Laura K Muehlbauer, Evgenia Shishkova, Katherine A Overmyer, Joshua J Coon, David J Pagliarini.

Coenzyme Q (CoQ, ubiquinone) is an essential cellular cofactor comprised of a redox-active quinone head group and a long hydrophobic polyisoprene tail. How mitochondria access cytosolic isoprenoids for CoQ biosynthesis is a longstanding mystery. Here, via a combination of genetic screening, metabolic tracing, and targeted uptake assays, we reveal that Hem25p-a mitochondrial glycine transporter required for heme biosynthesis-doubles as an isopentenyl pyrophosphate (IPP) transporter in Saccharomyces cerevisiae . Mitochondria lacking Hem25p fail to efficiently incorporate IPP into early CoQ precursors, leading to loss of CoQ and turnover of CoQ biosynthetic proteins. Expression of Hem25p in Escherichia coli enables robust IPP uptake demonstrating that Hem25p is sufficient for IPP transport. Collectively, our work reveals that Hem25p drives the bulk of mitochondrial isoprenoid transport for CoQ biosynthesis in yeast.

DOI: https://doi.org/10.1101/2023.03.14.532620
Curr Biol. 2023 Mar 27. pii: S0960-9822(23)00177-X. [Epub ahead of print]33(6): R219-R221

Evolution: 'Millefoglie' origin of mitochondrial cristae.

Paul A M Michels, Michael L Ginger.

Striated intracytoplasmic membranes in alphaproteobacteria are often reminiscent of millefoglie pastries. A new study reveals a protein complex homologous to that responsible for mitochondrial cristae formation drives intracytoplasmic membrane formation, thereby establishing bacterial ancestry for the biogenesis of mitochondrial cristae.

DOI: https://doi.org/10.1016/j.cub.2023.02.037
Nat Chem Biol. 2023 Mar 27.

Cytosolic and mitochondrial NADPH fluxes are independently regulated.

Xiangfeng Niu, Ethan Stancliffe, Susan J Gelman, Lingjue Wang, Michaela Schwaiger-Haber, Joe L Rowles, Leah P Shriver, Gary J Patti.

Although nicotinamide adenine dinucleotide phosphate (NADPH) is produced and consumed in both the cytosol and mitochondria, the relationship between NADPH fluxes in each compartment has been difficult to assess due to technological limitations. Here we introduce an approach to resolve cytosolic and mitochondrial NADPH fluxes that relies on tracing deuterium from glucose to metabolites of proline biosynthesis localized to either the cytosol or mitochondria. We introduced NADPH challenges in either the cytosol or mitochondria of cells by using isocitrate dehydrogenase mutations, administering chemotherapeutics or with genetically encoded NADPH oxidase. We found that cytosolic challenges influenced NADPH fluxes in the cytosol but not NADPH fluxes in mitochondria, and vice versa. This work highlights the value of using proline labeling as a reporter system to study compartmentalized metabolism and reveals that NADPH homeostasis in the cytosolic and mitochondrial locations of a cell are independently regulated, with no evidence for NADPH shuttle activity.

DOI: https://doi.org/10.1038/s41589-023-01283-9
Cell Metab. 2023 Mar 21. pii: S1550-4131(23)00082-7. [Epub ahead of print]

SUCNR1 signaling in adipocytes controls energy metabolism by modulating circadian clock and leptin expression.

Teresa Villanueva-Carmona, Lídia Cedó, Ana Madeira, Victòria Ceperuelo-Mallafré, M-Mar Rodríguez-Peña, Catalina Núñez-Roa, Elsa Maymó-Masip, Maria Repollés-de-Dalmau, Joan Badia, Noelia Keiran, Mercedes Mirasierra, Carolina Pimenta-Lopes, Joan Sabadell-Basallote, Ramón Bosch, Laura Caubet, Joan Carles Escolà-Gil, José-Manuel Fernández-Real, Nuria Vilarrasa, Francesc Ventura, Mario Vallejo, Joan Vendrell, Sonia Fernández-Veledo.

  Adipose tissue modulates energy homeostasis by secreting leptin, but little is known about the factors governing leptin production. We show that succinate, long perceived as a mediator of immune response and lipolysis, controls leptin expression via its receptor SUCNR1. Adipocyte-specific deletion of Sucnr1 influences metabolic health according to nutritional status. Adipocyte Sucnr1 deficiency impairs leptin response to feeding, whereas oral succinate mimics nutrient-related leptin dynamics via SUCNR1. SUCNR1 activation controls leptin expression via the circadian clock in an AMPK/JNK-C/EBPα-dependent manner. Although the anti-lipolytic role of SUCNR1 prevails in obesity, its function as a regulator of leptin signaling contributes to the metabolically favorable phenotype in adipocyte-specific Sucnr1 knockout mice under standard dietary conditions. Obesity-associated hyperleptinemia in humans is linked to SUCNR1 overexpression in adipocytes, which emerges as the major predictor of adipose tissue leptin expression. Our study establishes the succinate/SUCNR1 axis as a metabolite-sensing pathway mediating nutrient-related leptin dynamics to control whole-body homeostasis.

Keywords:  GPCR; SUCNR1; adipocyte; adipose tissue; circadian clock; leptin; metabolism; metabolite; obesity; succinate

DOI:  https://doi.org/10.1016/j.cmet.2023.03.004
Hepatology. 2023 Apr 03.

Membrane phospholipid remodeling modulates nonalcoholic steatohepatitis progression by regulating mitochondrial homeostasis.

Ye Tian, Matthew J Jellinek, Kritika Mehta, Sun Mi Seok, Shanny Hsuan Kuo, Wei Lu, Ruicheng Shi, Richard Lee, Gee W Lau, Jongsook Kim Kemper, Kai Zhang, David A Ford, Bo Wang.

BACKGROUND AIMS: Nonalcoholic steatohepatitis (NASH), characterized by inflammation and fibrosis, is emerging as a leading etiology of hepatocellular carcinoma (HCC). Lipidomics analyses in the liver have shown that the levels of polyunsaturated phosphatidylcholine (PC) are decreased in NASH patients, but the roles of membrane PC composition in the pathogenesis of NASH has not been investigated. Lysophosphatidylcholine acyltransferase 3 (LPCAT3), a phospholipid (PL) remodeling enzyme that produces polyunsaturated PLs, is a major determinant of membrane PC content in the liver.
APPROACH RESULTS: The expression of LPCAT3 and the correlation between its expression and NASH severity were analyzed in human patient samples. We examined the effect of Lpcat3 deficiency on NASH progression using Lpcat3 liver specific knockout mice (LKO). RNA sequencing, lipidomics, and metabolomics were performed in liver samples. Primary hepatocytes and hepatic cell lines were used for in vitro analyses. We show that LPCAT3 is dramatically suppressed in human NASH livers, and its expression is inversely correlated with NAFLD activity score and fibrosis stage. Loss of Lpcat3 in mouse liver promotes both spontaneous and diet-induced NASH/HCC. Mechanistically, Lpcat3 deficiency enhances reactive oxygen species production due to impaired mitochondrial homeostasis. Loss of Lpcat3 increases inner mitochondrial membrane PL saturation and elevates stress-induced autophagy, resulting in reduced mitochondrial content and increased fragmentation. Furthermore, overexpressing Lpcat3 in the liver ameliorates inflammation and fibrosis of NASH.
CONCLUSIONS: These results demonstrate that membrane PL composition modulates the progression of NASH and that manipulating LPCAT3 expression could be an effective therapeutic for NASH.

DOI: https://doi.org/10.1097/HEP.0000000000000375