bims-camemi Biomed News
on Mitochondrial metabolism in cancer
Issue of 2020‒07‒05
forty-two papers selected by
Christian Frezza
University of Cambridge, MRC Cancer Unit


  1. Nature. 2020 Jul 01.
    Napolitano G, Di Malta C, Esposito A, de Araujo MEG, Pece S, Bertalot G, Matarese M, Benedetti V, Zampelli A, Stasyk T, Siciliano D, Venuta A, Cesana M, Vilardo C, Nusco E, Monfregola J, Calcagnì A, Di Fiore PP, Huber LA, Ballabio A.
      The mechanistic target of rapamycin complex 1 (mTORC1) is a key metabolic hub that controls the cellular response to environmental cues by exerting its kinase activity on multiple substrates1-3. However, whether mTORC1 responds to diverse stimuli by differentially phosphorylating specific substrates is poorly understood. Here we show that transcription factor EB (TFEB), a master regulator of lysosomal biogenesis and autophagy4,5, is phosphorylated by mTORC1 via a substrate-specific mechanism that is mediated by Rag GTPases. Owing to this mechanism, the phosphorylation of TFEB-unlike other substrates of mTORC1, such as S6K and 4E-BP1- is strictly dependent on the amino-acid-mediated activation of RagC and RagD GTPases, but is insensitive to RHEB activity induced by growth factors. This mechanism has a crucial role in Birt-Hogg-Dubé syndrome, a disorder that is caused by mutations in the RagC and RagD activator folliculin (FLCN) and is characterized by benign skin tumours, lung and kidney cysts and renal cell carcinoma6,7. We found that constitutive activation of TFEB is the main driver of the kidney abnormalities and mTORC1 hyperactivity in a mouse model of Birt-Hogg-Dubé syndrome. Accordingly, depletion of TFEB in kidneys of these mice fully rescued the disease phenotype and associated lethality, and normalized mTORC1 activity. Our findings identify a mechanism that enables differential phosphorylation of mTORC1 substrates, the dysregulation of which leads to kidney cysts and cancer.
    DOI:  https://doi.org/10.1038/s41586-020-2444-0
  2. Proc Natl Acad Sci U S A. 2020 Jun 29. pii: 202000640. [Epub ahead of print]
    Ghosh S, Basu Ball W, Madaris TR, Srikantan S, Madesh M, Mootha VK, Gohil VM.
      Calcium uptake by the mitochondrial calcium uniporter coordinates cytosolic signaling events with mitochondrial bioenergetics. During the past decade all protein components of the mitochondrial calcium uniporter have been identified, including MCU, the pore-forming subunit. However, the specific lipid requirements, if any, for the function and formation of this channel complex are currently not known. Here we utilize yeast, which lacks the mitochondrial calcium uniporter, as a model system to address this problem. We use heterologous expression to functionally reconstitute human uniporter machinery both in wild-type yeast as well as in mutants defective in the biosynthesis of phosphatidylethanolamine, phosphatidylcholine, or cardiolipin (CL). We uncover a specific requirement of CL for in vivo reconstituted MCU stability and activity. The CL requirement of MCU is evolutionarily conserved with loss of CL triggering rapid turnover of MCU homologs and impaired calcium transport. Furthermore, we observe reduced abundance and activity of endogenous MCU in mammalian cellular models of Barth syndrome, which is characterized by a partial loss of CL. MCU abundance is also decreased in the cardiac tissue of Barth syndrome patients. Our work raises the hypothesis that impaired mitochondrial calcium transport contributes to the pathogenesis of Barth syndrome, and more generally, showcases the utility of yeast phospholipid mutants in dissecting the phospholipid requirements of ion channel complexes.
    Keywords:  Barth syndrome; EMRE; cardiolipin; mitochondrial calcium uniporter (MCU); uniplex
    DOI:  https://doi.org/10.1073/pnas.2000640117
  3. Cancer Discov. 2020 Jun 30. pii: CD-20-0226. [Epub ahead of print]
    Nagashima H, Lee CK, Tateishi K, Higuchi F, Subramanian M, Rafferty S, Melamed L, Miller JJ, Wakimoto H, Cahill DP.
      Nicotinamide adenine dinucleotide (NAD+) is an essential cofactor metabolite and is the currency of metabolic transactions critical for cell survival. Depending on tissue context and genotype, cancer cells have unique dependencies on NAD+ metabolic pathways. Poly(ADP-ribose) polymerases (PARPs) catalyze oligomerization of NAD+ monomers into poly(ADP-ribose) (PAR) chains during cellular response to alkylating chemotherapeutics, including procarbazine or temozolomide. Here, we find that, in endogenous IDH1 mutant tumor models, alkylator-induced cytotoxicity is markedly augmented by pharmacologic inhibition or genetic knockout of the PAR breakdown enzyme poly(ADP-ribose) glycohydrolase (PARG). Both in vitro and in vivo, we observe that concurrent alkylator and PARG inhibition depletes freely available NAD+ by preventing PAR breakdown, resulting in NAD+ sequestration and collapse of metabolic homeostasis. This effect reversed with NAD+ rescue supplementation, confirming the mechanistic basis of cytotoxicity. Thus, alkylating chemotherapy exposes a genotype-specific metabolic weakness in tumor cells that can be exploited by PARG inactivation.
    DOI:  https://doi.org/10.1158/2159-8290.CD-20-0226
  4. Redox Biol. 2020 Jun 21. pii: S2213-2317(20)30811-9. [Epub ahead of print]36 101606
    Chowdhury AR, Zielonka J, Kalyanaraman B, Hartley RC, Murphy MP, Avadhani NG.
      The mitochondrial electron transport chain is a major source of reactive oxygen species (ROS) and is also a target of ROS, with an implied role in the stabilization of hypoxia-inducible factor (HIF) and induction of the AMPK pathway. Here we used varying doses of two agents, Mito-Paraquat and Mito-Metformin, that have been conjugated to cationic triphenylphosphonium (TPP+) moiety to selectively target them to the mitochondrial matrix compartment, thereby resulting in the site-specific generation of ROS within mitochondria. These agents primarily induce superoxide (O2•-) production by acting on complex I. In Raw264.7 macrophages, C2C12 skeletal myocytes, and HCT116 adenocarcinoma cells, we show that mitochondria-targeted oxidants can induce ROS (O2•- and H2O2). In all three cell lines tested, the mitochondria-targeted agents disrupted membrane potential and activated calcineurin and the Cn-dependent retrograde signaling pathway. Hypoxic culture conditions also induced Cn activation and HIF1α activation in a temporally regulated manner, with the former appearing at shorter exposure times. Together, our results indicate that mitochondrial oxidant-induced retrograde signaling is driven by disruption of membrane potential and activation of Ca2+/Cn pathway and is independent of ROS-induced HIF1α or AMPK pathways.
    Keywords:  Calcineurin activation; HIF1α; Hypoxia mediated stress; Macrophage cell line; Mitochondria targeted agents; Mitochondrial ROS; Retrograde signaling
    DOI:  https://doi.org/10.1016/j.redox.2020.101606
  5. Front Endocrinol (Lausanne). 2020 ;11 374
    Yu R, Lendahl U, Nistér M, Zhao J.
      Mitochondria are highly dynamic organelles and important for a variety of cellular functions. They constantly undergo fission and fusion events, referred to as mitochondrial dynamics, which affects the shape, size, and number of mitochondria in the cell, as well as mitochondrial subcellular transport, mitochondrial quality control (mitophagy), and programmed cell death (apoptosis). Dysfunctional mitochondrial dynamics is associated with various human diseases. Mitochondrial dynamics is mediated by a set of mitochondria-shaping proteins in both yeast and mammals. In this review, we describe recent insights into the potential molecular mechanisms underlying mitochondrial fusion and fission, particularly highlighting the coordinating roles of different mitochondria-shaping proteins in the processes, as well as the roles of the endoplasmic reticulum (ER), the actin cytoskeleton and membrane phospholipids in the regulation of mitochondrial dynamics. We particularly focus on emerging roles for the mammalian mitochondrial proteins Fis1, Mff, and MIEFs (MIEF1 and MIEF2) in regulating the recruitment of the cytosolic Drp1 to the surface of mitochondria and how these proteins, especially Fis1, mediate crosstalk between the mitochondrial fission and fusion machineries. In summary, this review provides novel insights into the molecular mechanisms of mammalian mitochondrial dynamics and the involvement of these mechanisms in apoptosis and autophagy.
    Keywords:  apoptosis; fission; fusion; mitochondrial dynamics; mitophagy
    DOI:  https://doi.org/10.3389/fendo.2020.00374
  6. Cancers (Basel). 2020 Jun 26. pii: E1703. [Epub ahead of print]12(6):
    Braga M, Kaliszczak M, Carroll L, Schug ZT, Heinzmann K, Baxan N, Benito A, Valbuena GN, Stribbling S, Beckley A, Mackay G, Mauri F, Latigo J, Barnes C, Keun H, Gottlieb E, Aboagye EO.
      The monocarboxylate transporter 1 (MCT1) is a key element in tumor cell metabolism and inhibition of MCT1 with AZD3965 is undergoing clinical trials. We aimed to investigate nutrient fluxes associated with MCT1 inhibition by AZD3965 to identify possible biomarkers of drug action. We synthesized an 18F-labeled lactate analogue, [18F]-S-fluorolactate ([18F]-S-FL), that was used alongside [18F]fluorodeoxyglucose ([18F]FDG), and 13C-labeled glucose and lactate, to investigate the modulation of metabolism with AZD3965 in diffuse large B-cell lymphoma models in NOD/SCID mice. Comparative analysis of glucose and lactate-based probes showed a preference for glycolytic metabolism in vitro, whereas in vivo, both glucose and lactate were used as metabolic fuel. While intratumoral L-[1-13C]lactate and [18F]-S-FL were unchanged or lower at early (5 or 30 min) timepoints, these variables were higher compared to vehicle controls at 4 h following treatment with AZD3965, which indicates that inhibition of MCT1-mediated lactate import is reversed over time. Nonetheless, AZD3965 treatment impaired DLBCL tumor growth in mice. This was hypothesized to be a consequence of metabolic strain, as AZD3965 treatment showed a reduction in glycolytic intermediates and inhibition of the TCA cycle likely due to downregulated PDH activity. Glucose ([18F]FDG and D-[13C6]glucose) and lactate-based probes ([18F]-S-FL and L-[1-13C]lactate) can be successfully used as biomarkers for AZD3965 treatment.
    Keywords:  AZD3965; cancer metabolism; diffuse large B-cell lymphoma; glycolysis; lactate; metabolic flux; monocarboxylate transporter 1; positron emission tomography (PET)
    DOI:  https://doi.org/10.3390/cancers12061703
  7. Dev Cell. 2020 Jun 30. pii: S1534-5807(20)30460-3. [Epub ahead of print]
    Shin HR, Zoncu R.
      The lysosome is an essential catabolic organelle that consumes cellular biomass to regenerate basic building blocks that can fuel anabolic reactions. This simple view has evolved more recently to integrate novel functions of the lysosome as a key signaling center, which can steer the metabolic trajectory of cells in response to changes in nutrients, growth factors, and stress. Master protein kinases and transcription factors mediate the growth-promoting and catabolic activities of the lysosome and undergo a complex interplay that enables cellular adaptation to ever-changing metabolic conditions. Understanding how this coordination occurs will shed light on the fundamental logic of how the lysosome functions to control growth in the context of development, tissue homeostasis, and cancer.
    Keywords:  TFEB; anabolism; autophagy; catabolism; lysosome; mTORC1; nutrient sensing
    DOI:  https://doi.org/10.1016/j.devcel.2020.06.010
  8. DNA Cell Biol. 2020 Jun 26.
    Vianello C, Cocetta V, Caicci F, Boldrin F, Montopoli M, Martinuzzi A, Carelli V, Giacomello M.
      Mitochondria contain their own genome, mitochondrial DNA (mtDNA), essential to support their fundamental intracellular role in ATP production and other key metabolic and homeostatic pathways. Mitochondria are highly dynamic organelles that communicate with all the other cellular compartments, through sites of high physical proximity. Among all, their crosstalk with the endoplasmic reticulum (ER) appears particularly important as its derangement is tightly implicated with several human disorders. Population-specific mtDNA variants clustered in defining the haplogroups have been shown to exacerbate or mitigate these pathological conditions. The exact mechanisms of the mtDNA background-modifying effect are not completely clear and a possible explanation is the outcome of mitochondrial efficiency on retrograde signaling to the nucleus. However, the possibility that different haplogroups shape the proximity and crosstalk between mitochondria and the ER has never been proposed neither investigated. In this study, we pose and discuss this question and provide preliminary data to answer it. Besides, we also address the possibility that single, disease-causing mtDNA point mutations may act also by reshaping organelle communication. Overall, this perspective review provides a theoretical platform for future studies on the interaction between mtDNA variants and organelle contact sites.
    Keywords:  LHON disease; haplogroup; mitochondria/ER contacts; mtDNA
    DOI:  https://doi.org/10.1089/dna.2020.5614
  9. Front Physiol. 2020 ;11 677
    Lai N, Fealy CE, Kummitha CM, Cabras S, Kirwan JP, Hoppel CL.
      Aim: Insulin-resistant skeletal muscle is characterized by metabolic inflexibility with associated alterations in substrate selection, mediated by peroxisome-proliferator activated receptor δ (PPARδ). Although it is established that PPARδ contributes to the alteration of energy metabolism, it is not clear whether it plays a role in mitochondrial fuel competition. While nutrient overload may impair metabolic flexibility by fuel congestion within mitochondria, in absence of obesity defects at a mitochondrial level have not yet been excluded. We sought to determine whether reduced PPARδ content in insulin-resistant rat skeletal muscle of a non-obese rat model of T2DM (Goto-Kakizaki, GK) ameliorate the inhibitory effect of fatty acid (i.e., palmitoylcarnitine) on mitochondrial carbohydrate oxidization (i.e., pyruvate) in muscle fibers.Methods: Bioenergetic function was characterized in oxidative soleus (S) and glycolytic white gastrocnemius (WG) muscles with measurement of respiration rates in permeabilized fibers in the presence of complex I, II, IV, and fatty acid substrates. Mitochondrial content was measured by citrate synthase (CS) and succinate dehydrogenase activity (SDH). Western blot was used to determine protein expression of PPARδ, PDK isoform 2 and 4.
    Results: CS and SDH activity, key markers of mitochondrial content, were reduced by ∼10-30% in diabetic vs. control, and the effect was evident in both oxidative and glycolytic muscles. PPARδ (p < 0.01), PDK2 (p < 0.01), and PDK4 (p = 0.06) protein content was reduced in GK animals compared to Wistar rats (N = 6 per group). Ex vivo respiration rates in permeabilized muscle fibers determined in the presence of complex I, II, IV, and fatty acid substrates, suggested unaltered mitochondrial bioenergetic function in T2DM muscle. Respiration in the presence of pyruvate was higher compared to palmitoylcarnitine in both animal groups and fiber types. Moreover, respiration rates in the presence of both palmitoylcarnitine and pyruvate were reduced by 25 ± 6% (S), 37 ± 6% (WG) and 63 ± 6% (S), 57 ± 8% (WG) compared to pyruvate for both controls and GK, respectively. The inhibitory effect of palmitoylcarnitine on respiration was significantly greater in GK than controls (p < 10-3).
    Conclusion: With competing fuels, the presence of fatty acids diminishes mitochondria ability to utilize carbohydrate derived substrates in insulin-resistant muscle despite reduced PPARδ content.
    Keywords:  bioenergetic; diabetes; fatty acid oxidation; metabolic flexibility; oxidative phosphorylation
    DOI:  https://doi.org/10.3389/fphys.2020.00677
  10. Front Oncol. 2020 ;10 807
    Prado-Garcia H, Campa-Higareda A, Romero-Garcia S.
      Lactic acidosis (3 to 40 mM, pH < 6.9) is a condition found in solid tumors because tumor cells have a high rate of glucose consumption and lactate production even in the presence of oxygen; nevertheless, the microenvironment might still provide a sufficient glucose supply. Lactic acidosis has been proposed to shift metabolism from aerobic glycolysis toward oxidative phosphorylation (OXPHOS). We tested if lung tumor cells cultured under lactic acidosis shift their metabolism from glycolysis to OXPHOS by consuming extracellular lactate, increasing growth rate. We analyzed lung adenocarcinoma (A-549, A-427) cell lines and non-transformed fibroblast cells (MRC-5), which were cultured using RPMI-1640 medium initially containing lactate (2 mM) and glucose (10 mM), at pH 7.2 or 6.2 and oxygen tension 21% O2 (normoxia) or 2% O2 (hypoxia). We obtained growth curves, as well as glucose consumption and lactate production rates (measured during exponential growth) for each cell line. HIF-1α (Hypoxia-inducible factor 1 α), CS (citrate synthase) and AMPK (AMP-activated protein kinase) transcript levels were analyzed using RT-qPCR. By flow cytometry, we determined: (a) expression of glucose transporters (GLUT)1 and 4; (b) lactate transporters (MCT)1 and 4; (c) cell cycle profile, and (d) protein levels of HIF-1α, total and phosphorylated AMPK (pAMPK). Mitochondrial functionality was evaluated by measuring O2 consumption in tumor cells using polarography and a Clark-type electrode. Tumor and non-transformed cells used both aerobic glycolysis and OXPHOS for obtaining energy. As of 48 h of culture, lactate levels ranged from (4.5-14 mM), thus forming a lactic environment. Lactic acidosis diminished GLUT1/GLUT4 expression and glucose consumption in A-549, but not in A-427 cells, and induced differential expression of HIF-1α, AMPK, and CS transcripts. A-427 cells increased pAMPK and HIF-1α levels and shifted their metabolism increasing OXPHOS; thus supporting cell growth. Conversely, A-549 cells increased HIF-1α protein levels, but did not activate AMPK and diminished OXPHOS. A-549 cells survived by arresting cells in G1-phase. Our findings show that lactic acidosis diminishes Warburg effect in tumor cells, but this change does not necessarily promote a shift to OXPHOS. Hence, lung adenocarcinomas show a differential metabolic response even when they are under the same microenvironmental conditions.
    Keywords:  aerobic glycolysis; mitochondrial function; oxidative metabolism; tumor metabolic shift; tumor metabolic symbiosis
    DOI:  https://doi.org/10.3389/fonc.2020.00807
  11. Cell. 2020 Jun 24. pii: S0092-8674(20)30745-5. [Epub ahead of print]
    Wu L, Hollinshead KER, Hao Y, Au C, Kroehling L, Ng C, Lin WY, Li D, Silva HM, Shin J, Lafaille JJ, Possemato R, Pacold ME, Papagiannakopoulos T, Kimmelman AC, Satija R, Littman DR.
      Targeting glycolysis has been considered therapeutically intractable owing to its essential housekeeping role. However, the context-dependent requirement for individual glycolytic steps has not been fully explored. We show that CRISPR-mediated targeting of glycolysis in T cells in mice results in global loss of Th17 cells, whereas deficiency of the glycolytic enzyme glucose phosphate isomerase (Gpi1) selectively eliminates inflammatory encephalitogenic and colitogenic Th17 cells, without substantially affecting homeostatic microbiota-specific Th17 cells. In homeostatic Th17 cells, partial blockade of glycolysis upon Gpi1 inactivation was compensated by pentose phosphate pathway flux and increased mitochondrial respiration. In contrast, inflammatory Th17 cells experience a hypoxic microenvironment known to limit mitochondrial respiration, which is incompatible with loss of Gpi1. Our study suggests that inhibiting glycolysis by targeting Gpi1 could be an effective therapeutic strategy with minimum toxicity for Th17-mediated autoimmune diseases, and, more generally, that metabolic redundancies can be exploited for selective targeting of disease processes.
    Keywords:  CRISPR; EAE; OXPHOS; autoimmunity; colitis; glycolysis; hypoxia; inflammation; metabolic plasticity; segmented filamentous bacteria
    DOI:  https://doi.org/10.1016/j.cell.2020.06.014
  12. Nat Commun. 2020 Jul 03. 11(1): 3326
    Ishak Gabra MB, Yang Y, Li H, Senapati P, Hanse EA, Lowman XH, Tran TQ, Zhang L, Doan LT, Xu X, Schones DE, Fruman DA, Kong M.
      Tumour cells adapt to nutrient deprivation in vivo, yet strategies targeting the nutrient poor microenvironment remain unexplored. In melanoma, tumour cells often experience low glutamine levels, which promote cell dedifferentiation. Here, we show that dietary glutamine supplementation significantly inhibits melanoma tumour growth, prolongs survival in a transgenic melanoma mouse model, and increases sensitivity to a BRAF inhibitor. Metabolomic analysis reveals that dietary uptake of glutamine effectively increases the concentration of glutamine in tumours and its downstream metabolite, αKG, without increasing biosynthetic intermediates necessary for cell proliferation. Mechanistically, we find that glutamine supplementation uniformly alters the transcriptome in tumours. Our data further demonstrate that increase in intra-tumoural αKG concentration drives hypomethylation of H3K4me3, thereby suppressing epigenetically-activated oncogenic pathways in melanoma. Therefore, our findings provide evidence that glutamine supplementation can serve as a potential dietary intervention to block melanoma tumour growth and sensitize tumours to targeted therapy via epigenetic reprogramming.
    DOI:  https://doi.org/10.1038/s41467-020-17181-w
  13. Sci Rep. 2020 Jun 30. 10(1): 10618
    Noh S, Phorl S, Naskar R, Oeum K, Seo Y, Kim E, Kweon HS, Lee JY.
      Mitochondria are dynamic organelles that undergo fusion and fission in response to various physiological and stress stimuli, which play key roles in diverse mitochondrial functions such as energy metabolism, intracellular signaling, and apoptosis. OPA1, a mitochondrial dynamin-like GTPase, is responsible for the inner membrane fusion of mitochondria, and the function of OPA1 is regulated by proteolytic cleavage in response to various metabolic stresses. Growing evidences highlighted the importance of mitochondrial adaptation in response to metabolic stimuli. Here, we demonstrated the role of p32/C1QBP in mitochondrial morphology by regulating OMA1-dependent proteolytic processing of OPA1. Genetic ablation of p32/C1QBP activates OMA1, cleaves OPA1, and leads mitochondrial fragmentation and swelling. The loss of p32/C1QBP decreased mitochondrial respiration and lipid utilization, sensitized cells to mitochondrial stress, and triggered a metabolic shift from oxidative phosphorylation to glycolysis, which were correlated with apoptosis in cancer cells and the inhibition of 3D-spheroid formation. These results suggest a unique regulation of cell physiology by mitochondria and provide a basis for a new therapeutic strategy for cancer.
    DOI:  https://doi.org/10.1038/s41598-020-67457-w
  14. PLoS Biol. 2020 Jun;18(6): e3000732
    Gutiérrez-Salmerón M, García-Martínez JM, Martínez-Useros J, Fernández-Aceñero MJ, Viollet B, Olivier S, Chauhan J, Lucena SR, De la Vieja A, Goding CR, Chocarro-Calvo A, García-Jiménez C.
      Coordination of gene expression with nutrient availability supports proliferation and homeostasis and is shaped by protein acetylation. Yet how physiological/pathological signals link acetylation to specific gene expression programs and whether such responses are cell-type-specific is unclear. AMP-activated protein kinase (AMPK) is a key energy sensor, activated by glucose limitation to resolve nutrient supply-demand imbalances, critical for diabetes and cancer. Unexpectedly, we show here that, in gastrointestinal cancer cells, glucose activates AMPK to selectively induce EP300, but not CREB-binding protein (CBP). Consequently, EP300 is redirected away from nuclear receptors that promote differentiation towards β-catenin, a driver of proliferation and colorectal tumorigenesis. Importantly, blocking glycogen synthesis permits reactive oxygen species (ROS) accumulation and AMPK activation in response to glucose in previously nonresponsive cells. Notably, glycogen content and activity of the ROS/AMPK/EP300/β-catenin axis are opposite in healthy versus tumor sections. Glycogen content reduction from healthy to tumor tissue may explain AMPK switching from tumor suppressor to activator during tumor evolution.
    DOI:  https://doi.org/10.1371/journal.pbio.3000732
  15. J Biol Chem. 2020 Jul 01. pii: jbc.AC120.014189. [Epub ahead of print]
    Lafita-Navarro MC, Perez-Castro L, Zacharias LG, Barnes S, DeBerardinis RJ, Conacci-Sorrell M.
      The transcription factor aryl hydrocarbon receptor (AHR) drives the expression of genes involved in detoxification pathways in cells exposed to pollutants and other small molecules. Moreover, AHR supports transcriptional programs that promote ribosome biogenesis and protein synthesis in cells stimulated to proliferate by the oncoprotein MYC. Thus, AHR is necessary for the proliferation of MYC-overexpressing cells. To define metabolic pathways in which AHR cooperates with MYC in supporting cell growth, here we used LC-MS-based metabolomics to examine the metabolome of MYC-expressing cells uponAHR knockdown. We found that AHR knockdown reduced lactate, S-lactoyl-glutathione,N-acetyl-L-alanine, 2-hydroxyglutarate, and uridine-5-monophosphate (UMP) levels. Using our previously obtained RNA-seq data, we found that AHR mediates the expression of the UMP-generating enzymes dihydroorotate dehydrogenase (quinone) (DHODH) and uridine monophosphate synthetase (UMPS), as well as lactate dehydrogenase A (LDHA), establishing a mechanism by which AHR regulates lactate and UMP production in MYC-overexpressing cells. AHR knockdown in glioblastoma cells also reduced the expression of LDHA (and lactate), DHODH,and UMPS, but did not affect UMP levels, likely due to compensatory mechanisms in these cells. Our results indicate that AHR contributes to the regulation of metabolic pathways necessary for the proliferation of transformed cells.
    Keywords:  Myc (c-Myc); aryl hydrocarbon receptor (AhR) (AHR); cancer; gene regulation; glioblastoma; glycolysis; metabolism; metabolomics; oncogene; pyrimidine
    DOI:  https://doi.org/10.1074/jbc.AC120.014189
  16. Sci Rep. 2020 Jun 29. 10(1): 10304
    Lee JW.
      For decades, it was not entirely clear why mitochondria develop cristae? The work employing the transmembrane-electrostatic proton localization theory reported here has now provided a clear answer to this fundamental question. Surprisingly, the transmembrane-electrostatically localized proton concentration at a curved mitochondrial crista tip can be significantly higher than that at the relatively flat membrane plane regions where the proton-pumping respiratory supercomplexes are situated. The biological significance for mitochondrial cristae has now, for the first time, been elucidated at a protonic bioenergetics level: 1) The formation of cristae creates more mitochondrial inner membrane surface area and thus more protonic capacitance for transmembrane-electrostatically localized proton energy storage; and 2) The geometric effect of a mitochondrial crista enhances the transmembrane-electrostatically localized proton density to the crista tip where the ATP synthase can readily utilize the localized proton density to drive ATP synthesis.
    DOI:  https://doi.org/10.1038/s41598-020-66203-6
  17. Trends Biochem Sci. 2020 Jun 25. pii: S0968-0004(20)30145-6. [Epub ahead of print]
    Cambronne XA, Kraus WL.
      The numerous biological roles of NAD+ are organized and coordinated via its compartmentalization within cells. The spatial and temporal partitioning of this intermediary metabolite is intrinsic to understanding the impact of NAD+ on cellular signaling and metabolism. We review evidence supporting the compartmentalization of steady-state NAD+ levels in cells, as well as how the modulation of NAD+ synthesis dynamically regulates signaling by controlling subcellular NAD+ concentrations. We further discuss potential benefits to the cell of compartmentalizing NAD+, and methods for measuring subcellular NAD+ levels.
    Keywords:  CD38; nicotinamide mononucleotide adenylyltransferase (NMNAT); nicotinamide phosphoribosyltransferase (NAMPT); poly(ADP-ribose) polymerase (PARP); sirtuin
    DOI:  https://doi.org/10.1016/j.tibs.2020.05.010
  18. Sci Signal. 2020 Jun 30. pii: eaax6660. [Epub ahead of print]13(638):
    Gutiérrez T, Qi H, Yap MC, Tahbaz N, Milburn LA, Lucchinetti E, Lou PH, Zaugg M, LaPointe PG, Mercier P, Overduin M, Bischof H, Burgstaller S, Malli R, Ballanyi K, Shuai J, Simmen T.
      Chaperones in the endoplasmic reticulum (ER) control the flux of Ca2+ ions into mitochondria, thereby increasing or decreasing the energetic output of the oxidative phosphorylation pathway. An example is the abundant ER lectin calnexin, which interacts with sarco/endoplasmic reticulum Ca2+ ATPase (SERCA). We found that calnexin stimulated the ATPase activity of SERCA by maintaining its redox state. This function enabled calnexin to control how much ER Ca2+ was available for mitochondria, a key determinant for mitochondrial bioenergetics. Calnexin-deficient cells compensated for the loss of this function by partially shifting energy generation to the glycolytic pathway. These cells also showed closer apposition between the ER and mitochondria. Calnexin therefore controls the cellular energy balance between oxidative phosphorylation and glycolysis.
    DOI:  https://doi.org/10.1126/scisignal.aax6660
  19. Cell Stem Cell. 2020 Jun 24. pii: S1934-5909(20)30272-1. [Epub ahead of print]
    Khoa LTP, Tsan YC, Mao F, Kremer DM, Sajjakulnukit P, Zhang L, Zhou B, Tong X, Bhanu NV, Choudhary C, Garcia BA, Yin L, Smith GD, Saunders TL, Bielas SL, Lyssiotis CA, Dou Y.
      Self-renewing embryonic stem cells (ESCs) respond to environmental cues by exiting pluripotency or entering a quiescent state. The molecular basis underlying this fate choice remains unclear. Here, we show that histone acetyltransferase MOF plays a critical role in this process through directly activating fatty acid oxidation (FAO) in the ground-state ESCs. We further show that the ground-state ESCs particularly rely on elevated FAO for oxidative phosphorylation (OXPHOS) and energy production. Mof deletion or FAO inhibition induces bona fide quiescent ground-state ESCs with an intact core pluripotency network and transcriptome signatures akin to the diapaused epiblasts in vivo. Mechanistically, MOF/FAO inhibition acts through reducing mitochondrial respiration (i.e., OXPHOS), which in turn triggers reversible pluripotent quiescence specifically in the ground-state ESCs. The inhibition of FAO/OXPHOS also induces quiescence in naive human ESCs. Our study suggests a general function of the MOF/FAO/OXPHOS axis in regulating cell fate determination in stem cells.
    Keywords:  FAO; MOF; cell fate decision; embryo development; epigenetics; quiescence; self-renewal; stem cell metabolism
    DOI:  https://doi.org/10.1016/j.stem.2020.06.005
  20. Cell. 2020 Jun 26. pii: S0092-8674(20)30753-4. [Epub ahead of print]
    Oguri Y, Shinoda K, Kim H, Alba DL, Bolus WR, Wang Q, Brown Z, Pradhan RN, Tajima K, Yoneshiro T, Ikeda K, Chen Y, Cheang RT, Tsujino K, Kim CR, Greiner VJ, Datta R, Yang CD, Atabai K, McManus MT, Koliwad SK, Spiegelman BM, Kajimura S.
      Adipose tissues dynamically remodel their cellular composition in response to external cues by stimulating beige adipocyte biogenesis; however, the developmental origin and pathways regulating this process remain insufficiently understood owing to adipose tissue heterogeneity. Here, we employed single-cell RNA-seq and identified a unique subset of adipocyte progenitor cells (APCs) that possessed the cell-intrinsic plasticity to give rise to beige fat. This beige APC population is proliferative and marked by cell-surface proteins, including PDGFRα, Sca1, and CD81. Notably, CD81 is not only a beige APC marker but also required for de novo beige fat biogenesis following cold exposure. CD81 forms a complex with αV/β1 and αV/β5 integrins and mediates the activation of integrin-FAK signaling in response to irisin. Importantly, CD81 loss causes diet-induced obesity, insulin resistance, and adipose tissue inflammation. These results suggest that CD81 functions as a key sensor of external inputs and controls beige APC proliferation and whole-body energy homeostasis.
    Keywords:  adipocyte progenitors; adipogenesis; beige fat; brown fat; diabetes; metabolic adaptation; metabolic disease; metabolism; obesity; tissue remodeling
    DOI:  https://doi.org/10.1016/j.cell.2020.06.021
  21. Nat Commun. 2020 Jul 03. 11(1): 3290
    Diederichs KA, Ni X, Rollauer SE, Botos I, Tan X, King MS, Kunji ERS, Jiang J, Buchanan SK.
      In mitochondria, β-barrel outer membrane proteins mediate protein import, metabolite transport, lipid transport, and biogenesis. The Sorting and Assembly Machinery (SAM) complex consists of three proteins that assemble as a 1:1:1 complex to fold β-barrel proteins and insert them into the mitochondrial outer membrane. We report cryoEM structures of the SAM complex from Myceliophthora thermophila, which show that Sam50 forms a 16-stranded transmembrane β-barrel with a single polypeptide-transport-associated (POTRA) domain extending into the intermembrane space. Sam35 and Sam37 are located on the cytosolic side of the outer membrane, with Sam35 capping Sam50, and Sam37 interacting extensively with Sam35. Sam35 and Sam37 each adopt a GST-like fold, with no functional, structural, or sequence similarity to their bacterial counterparts. Structural analysis shows how the Sam50 β-barrel opens a lateral gate to accommodate its substrates.
    DOI:  https://doi.org/10.1038/s41467-020-17144-1
  22. Nat Commun. 2020 Jul 03. 11(1): 3288
    Oh S, Yeom J, Cho HJ, Kim JH, Yoon SJ, Kim H, Sa JK, Ju S, Lee H, Oh MJ, Lee W, Kwon Y, Li H, Choi S, Han JH, Chang JH, Choi E, Kim J, Her NG, Kim SH, Kang SG, Paek E, Nam DH, Lee C, Kim HS.
      The prognostic and therapeutic relevance of molecular subtypes for the most aggressive isocitrate dehydrogenase 1/2 (IDH) wild-type glioblastoma (GBM) is currently limited due to high molecular heterogeneity of the tumors that impedes patient stratification. Here, we describe a distinct binary classification of IDH wild-type GBM tumors derived from a quantitative proteomic analysis of 39 IDH wild-type GBMs as well as IDH mutant and low-grade glioma controls. Specifically, GBM proteomic cluster 1 (GPC1) tumors exhibit Warburg-like features, neural stem-cell markers, immune checkpoint ligands, and a poor prognostic biomarker, FKBP prolyl isomerase 9 (FKBP9). Meanwhile, GPC2 tumors show elevated oxidative phosphorylation-related proteins, differentiated oligodendrocyte and astrocyte markers, and a favorable prognostic biomarker, phosphoglycerate dehydrogenase (PHGDH). Integrating these proteomic features with the pharmacological profiles of matched patient-derived cells (PDCs) reveals that the mTORC1/2 dual inhibitor AZD2014 is cytotoxic to the poor prognostic PDCs. Our analyses will guide GBM prognosis and precision treatment strategies.
    DOI:  https://doi.org/10.1038/s41467-020-17139-y
  23. Front Cell Dev Biol. 2020 ;8 381
    Otten ABC, Kamps R, Lindsey P, Gerards M, Pendeville-Samain H, Muller M, van Tienen FHJ, Smeets HJM.
      High mitochondrial DNA (mtDNA) copy numbers are essential for oogenesis and embryogenesis and correlate with fertility of oocytes and viability of embryos. To understand the pathology and mechanisms associated with low mtDNA copy numbers, we knocked down mitochondrial transcription factor A (tfam), a regulator of mtDNA replication, during early zebrafish development. Reduction of tfam using a splice-modifying morpholino (MO) resulted in a 42 ± 17% decrease in mtDNA copy number in embryos at 4 days post fertilization. Morphant embryos displayed abnormal development of the eye, brain, heart, and muscle, as well as a 50 ± 22% decrease in ATP production. Transcriptome analysis revealed a decrease in protein-encoding transcripts from the heavy strand of the mtDNA, and down-regulation of genes involved in haem production and the metabolism of metabolites, which appear to trigger increased rRNA and tRNA synthesis in the nucleoli. However, this stress or compensatory response appears to fall short as pathology emerges and expression of genes related to eye development are severely down-regulated. Taken together, this study highlights the importance of sufficient mtDNA copies for early zebrafish development. Zebrafish is an excellent model to manipulate the mtDNA bottleneck and study its effect on embryogenesis rapidly and in large numbers of offspring.
    Keywords:  OXPHOS deficiency; TFAM; mitochondria; mtDNA bottleneck; transcriptomics; zebrafish embryogenesis
    DOI:  https://doi.org/10.3389/fcell.2020.00381
  24. Trends Cancer. 2020 Jul;pii: S2405-8033(20)30083-2. [Epub ahead of print]6(7): 605-618
    Duan Q, Zhang H, Zheng J, Zhang L.
      Cancers develop within complex tissue environments consisting of diverse innate and adaptive immune cells, along with stromal cells, vascular networks, and many other cellular and noncellular components. The high heterogeneity within the tumor microenvironment (TME) remains a key obstacle in understanding and treating cancer. Understanding the dynamic functional interplay within this intricate ecosystem will provide important insights into the design of effective combinatorial strategies against cancer. Here, we present recent technical advances to explore the complexity of the TME. Then, we discuss how innate immune sensing machinery, genetic alterations of oncogenic signaling, cellular metabolism, and epigenetic factors are involved in modulating the TME. Finally, we summarize the potential strategies to boost antitumor immunity by therapeutically exploiting the TME.
    Keywords:  epigenetic; immune checkpoint blockade; metabolism; single cell profiling; tumor microenvironment
    DOI:  https://doi.org/10.1016/j.trecan.2020.02.022
  25. Proc Natl Acad Sci U S A. 2020 Jun 29. pii: 201915275. [Epub ahead of print]
    Pastor-Flores D, Talwar D, Pedre B, Dick TP.
      Peroxiredoxins are central to cellular redox homeostasis and signaling. They serve as peroxide scavengers, sensors, signal transducers, and chaperones, depending on conditions and context. Typical 2-Cys peroxiredoxins are known to switch between different oligomeric states, depending on redox state, pH, posttranslational modifications, and other factors. Quaternary states and their changes are closely connected to peroxiredoxin activity and function but so far have been studied, almost exclusively, outside the context of the living cell. Here we introduce the use of homo-FRET (Förster resonance energy transfer between identical fluorophores) fluorescence polarization to monitor dynamic changes in peroxiredoxin quaternary structure inside the crowded environment of living cells. Using the approach, we confirm peroxide- and thioredoxin-related quaternary transitions to take place in cellulo and observe that the relationship between dimer-decamer transitions and intersubunit disulfide bond formation is more complex than previously thought. Furthermore, we demonstrate the use of the approach to compare different peroxiredoxin isoforms and to identify mutations and small molecules affecting the oligomeric state inside cells. Mutagenesis experiments reveal that the dimer-decamer equilibrium is delicately balanced and can be shifted by single-atom structural changes. We show how to use this insight to improve the design of peroxiredoxin-based redox biosensors.
    Keywords:  dimer-decamer equilibrium; fluorescence polarization; homo-FRET; peroxiredoxins; protein oligomerization
    DOI:  https://doi.org/10.1073/pnas.1915275117
  26. Nat Commun. 2020 Jul 03. 11(1): 3347
    Assali EA, Jones AE, Veliova M, Acín-Pérez R, Taha M, Miller N, Shum M, Oliveira MF, Las G, Liesa M, Sekler I, Shirihai OS.
      A sharp increase in mitochondrial Ca2+ marks the activation of brown adipose tissue (BAT) thermogenesis, yet the mechanisms preventing Ca2+ deleterious effects are poorly understood. Here, we show that adrenergic stimulation of BAT activates a PKA-dependent mitochondrial Ca2+ extrusion via the mitochondrial Na+/Ca2+ exchanger, NCLX. Adrenergic stimulation of NCLX-null brown adipocytes (BA) induces a profound mitochondrial Ca2+ overload and impaired uncoupled respiration. Core body temperature, PET imaging of glucose uptake and VO2 measurements confirm a thermogenic defect in NCLX-null mice. We show that Ca2+ overload induced by adrenergic stimulation of NCLX-null BAT, triggers the mitochondrial permeability transition pore (mPTP) opening, leading to a remarkable mitochondrial swelling and cell death. Treatment with mPTP inhibitors rescue mitochondrial function and thermogenesis in NCLX-null BAT, while calcium overload persists. Our findings identify a key pathway through which BA evade apoptosis during adrenergic stimulation of uncoupling. NCLX deletion transforms the adrenergic pathway responsible for thermogenesis activation into a death pathway.
    DOI:  https://doi.org/10.1038/s41467-020-16572-3
  27. Front Cell Dev Biol. 2020 ;8 480
    Bhattacharya D, Scimè A.
      Mitochondria are crucial organelles that control cellular metabolism through an integrated mechanism of energy generation via oxidative phosphorylation. Apart from this canonical role, it is also integral for ROS production, fatty acid metabolism and epigenetic remodeling. Recently, a role for the mitochondria in effecting stem cell fate decisions has gained considerable interest. This is important for skeletal muscle, which exhibits a remarkable property for regeneration following injury, owing to satellite cells (SCs), the adult myogenic stem cells. Mitochondrial function is associated with maintaining and dictating SC fates, linked to metabolic programming during quiescence, activation, self-renewal, proliferation and differentiation. Notably, mitochondrial adaptation might take place to alter SC fates and function in the presence of different environmental cues. This review dissects the contribution of mitochondria to SC operational outcomes, focusing on how their content, function, dynamics and adaptability work to influence SC fate decisions.
    Keywords:  epigenetics; metabolism; mitochondria; myogenic stem cells; satellite cell fates
    DOI:  https://doi.org/10.3389/fcell.2020.00480
  28. Int J Biochem Cell Biol. 2020 Jun 25. pii: S1357-2725(20)30113-8. [Epub ahead of print] 105796
    Zheng T, Jäättelä M, Liu B.
      pH gradient reversal refers to intracellular alkalization and extracellular acidification commonly seen in malignant tumors. To meet their high anabolic demand, cancer cells rewire their glucose metabolism from oxidative phosphorylation to lactate fermentation, which results in the excessive generation of protons. To avoid lethal cytosolic acidification, lactate-fermenting cancer cells activate multiple acid removal pathways leading to the acidification of the extracellular space. This acidification is often further intensified by the defective capacity of the disorganized tumor vasculature to dilute protons away from the cancer tissue. The cancer-specific proton equilibrium with highly alkaline cytosol and acidic extracellular space is emerging as a fundamental driving force for cancer growth. Here, we discuss how cancer cells establish and maintain reversed pH gradient, how pH gradient reversal fuels cancer progression, and how these mechanisms can be targeted in cancer therapy.
    Keywords:  cancer; cellbiology; glycolysis; lysosome; pH gradient reversal
    DOI:  https://doi.org/10.1016/j.biocel.2020.105796
  29. Aging (Albany NY). 2020 Jun 29. 12
    Dong H, Qiang Z, Chai D, Peng J, Xia Y, Hu R, Jiang H.
      Acute lung injury (ALI) is a syndrome associated with a high mortality rate. Nrf2 is a key regulator of intracellular oxidation homeostasis that plays a pivotal role in controlling lipid peroxidation, which is closely related to the process of ferroptosis. However, the intrinsic effect of Nrf2 on ferroptosis remains to be investigated in ALI. We found that MDA expression increased while GSH and GPX4 decreased in ALI models. Furthermore, the characteristic mitochondrial morphological changes of ferroptosis appear in type II alveolar epithelial cells in IIR models. Additional pre-treatment of Fe and Ferrostatin-1 in ALI significantly aggravated or ameliorated the pathological injuries of lung tissue, pulmonary edema, lipid peroxidation, as well as promoted or prevented cell death, respectively. Knocking down Nrf2 notably decreased the expression of SLC7A11 and HO-1. Interference with SLC7A11 markedly increased Nrf2-HO-1 and dramatically attenuated cell death in OGD/R models. These findings indicate that ferroptosis can be inhibited by Nrf2 through regulating SLC7A11 and HO-1, which may provide a potential therapeutic strategy for IIR-ALI.
    Keywords:  acute lung injury; ferroptosis; heme oxygenase-1; solute carrier family 7 member 11; uclear factor erythroid 2 related factor2
    DOI:  https://doi.org/10.18632/aging.103378
  30. Cell Rep. 2020 Jun 30. pii: S2211-1247(20)30806-8. [Epub ahead of print]31(13): 107825
    Alam Z, Devalaraja S, Li M, To TKJ, Folkert IW, Mitchell-Velasquez E, Dang MT, Young P, Wilbur CJ, Silverman MA, Li X, Chen YH, Hernandez PT, Bhattacharyya A, Bhattacharya M, Levine MH, Haldar M.
      Activated macrophages must carefully calibrate their inflammatory responses to balance efficient pathogen control with inflammation-mediated tissue damage, but the molecular underpinnings of this "balancing act" remain unclear. Using genetically engineered mouse models and primary macrophage cultures, we show that Toll-like receptor (TLR) signaling induces the expression of the transcription factor Spic selectively in patrolling monocytes and tissue macrophages by a nuclear factor κB (NF-κB)-dependent mechanism. Functionally, Spic downregulates pro-inflammatory cytokines and promotes iron efflux by regulating ferroportin expression in activated macrophages. Notably, interferon-gamma blocks Spic expression in a STAT1-dependent manner. High levels of interferon-gamma are indicative of ongoing infection, and in its absence, activated macrophages appear to engage a "default" Spic-dependent anti-inflammatory pathway. We also provide evidence for the engagement of this pathway in sterile inflammation. Taken together, our findings uncover a pathway wherein counter-regulation of Spic by NF-κB and STATs attune inflammatory responses and iron metabolism in macrophages.
    Keywords:  Bach1; NF-κB; Spic; ferroportin; interferon-gamma; macrophages; monocytes
    DOI:  https://doi.org/10.1016/j.celrep.2020.107825
  31. EMBO J. 2020 Jun 30. e104820
    Kummer E, Ban N.
      Mitochondria are eukaryotic organelles of bacterial origin where respiration takes place to produce cellular chemical energy. These reactions are catalyzed by the respiratory chain complexes located in the inner mitochondrial membrane. Notably, key components of the respiratory chain complexes are encoded on the mitochondrial chromosome and their expression relies on a dedicated mitochondrial translation machinery. Defects in the mitochondrial gene expression machinery lead to a variety of diseases in humans mostly affecting tissues with high energy demand such as the nervous system, the heart, or the muscles. The mitochondrial translation system has substantially diverged from its bacterial ancestor, including alterations in the mitoribosomal architecture, multiple changes to the set of translation factors and striking reductions in otherwise conserved tRNA elements. Although a number of structures of mitochondrial ribosomes from different species have been determined, our mechanistic understanding of the mitochondrial translation cycle remains largely unexplored. Here, we present two cryo-EM reconstructions of human mitochondrial elongation factor G1 bound to the mammalian mitochondrial ribosome at two different steps of the tRNA translocation reaction during translation elongation. Our structures explain the mechanism of tRNA and mRNA translocation on the mitoribosome, the regulation of mtEFG1 activity by the ribosomal GTPase-associated center, and the basis of decreased susceptibility of mtEFG1 to the commonly used antibiotic fusidic acid.
    Keywords:  cryo-EM; elongation; mitoribosome; mtEFG1; translation
    DOI:  https://doi.org/10.15252/embj.2020104820
  32. Dev Cell. 2020 Jun 26. pii: S1534-5807(20)30461-5. [Epub ahead of print]
    Smith HJ, Sharma A, Mair WB.
      Aging is associated with a loss of metabolic homeostasis and plasticity, which is causally linked to multiple age-onset pathologies. The majority of the interventions-genetic, dietary, and pharmacological-that have been found to slow aging and protect against age-related disease in various organisms do so by targeting central metabolic pathways. However, targeting metabolic pathways chronically and ubiquitously makes it difficult to define the downstream effects responsible for lifespan extension and often results in negative effects on growth and health, limiting therapeutic potential. Insight into how metabolic signals are relayed between tissues, cells, and organelles opens up new avenues to target metabolic regulators locally rather than globally for healthy aging. In this review, we discuss the pro-longevity effects of targeting metabolic pathways in specific tissues and how these interventions communicate with distal cells to modulate aging. These studies may be crucial in designing interventions that promote longevity without negative health consequences.
    Keywords:  AMPK; NAD+; aging; extracellular vesicles; insulin signaling; mTOR; metabolism; microRNA; sirtuins; tissue-specificity
    DOI:  https://doi.org/10.1016/j.devcel.2020.06.011
  33. Cell Rep. 2020 Jun 30. pii: S2211-1247(20)30813-5. [Epub ahead of print]31(13): 107832
    Liao R, Zheng Y, Liu X, Zhang Y, Seim G, Tanimura N, Wilson GM, Hematti P, Coon JJ, Fan J, Xu J, Keles S, Bresnick EH.
      Protein ensembles control genome function by establishing, maintaining, and deconstructing cell-type-specific chromosomal landscapes. A plethora of small molecules orchestrate cellular functions and therefore may link physiological processes with genome biology. The metabolic enzyme and hemoglobin cofactor heme induces proteolysis of a transcriptional repressor, Bach1, and regulates gene expression post-transcriptionally. However, whether heme controls genome function broadly or through prescriptive actions is unclear. Using assay for transposase-accessible chromatin sequencing (ATAC-seq), we establish a heme-dependent chromatin atlas in wild-type and mutant erythroblasts lacking enhancers that confer normal heme synthesis. Amalgamating chromatin landscapes and transcriptomes in cells with sub-physiological heme and post-heme rescue reveals parallel Bach1-dependent and Bach1-independent mechanisms that target heme-sensing chromosomal hotspots. The hotspots harbor a DNA motif demarcating heme-regulated chromatin and genes encoding proteins not known to be heme regulated, including metabolic enzymes. The heme-omics analysis establishes how an essential biochemical cofactor controls genome function and cellular physiology.
    Keywords:  ATAC-seq; Bach1; GATA1; chromatin; erythroblast; erythroid; heme; transcriptome
    DOI:  https://doi.org/10.1016/j.celrep.2020.107832
  34. Proc Natl Acad Sci U S A. 2020 Jun 29. pii: 202002835. [Epub ahead of print]
    Chen X, Chen J, Yan B, Zhang W, Guddat LW, Liu X, Rao Z.
      FadE, an acyl-CoA dehydrogenase, introduces unsaturation to carbon chains in lipid metabolism pathways. Here, we report that FadE5 from Mycobacterium tuberculosis (MtbFadE5) and Mycobacterium smegmatis (MsFadE5) play roles in drug resistance and exhibit broad specificity for linear acyl-CoA substrates but have a preference for those with long carbon chains. Here, the structures of MsFadE5 and MtbFadE5, in the presence and absence of substrates, have been determined. These reveal the molecular basis for the broad substrate specificity of these enzymes. FadE5 interacts with the CoA region of the substrate through a large number of hydrogen bonds and an unusual π-π stacking interaction, allowing these enzymes to accept both short- and long-chain substrates. Residues in the substrate binding cavity reorient their side chains to accommodate substrates of various lengths. Longer carbon-chain substrates make more numerous hydrophobic interactions with the enzyme compared with the shorter-chain substrates, resulting in a preference for this type of substrate.
    Keywords:  acyl-CoA dehydrogenase; fatty acid; mycobacteria; tuberculosis
    DOI:  https://doi.org/10.1073/pnas.2002835117
  35. Antioxid Redox Signal. 2020 Jul 03.
    Selinski J, Scheibe R.
      Significance The importance of oxido-reductases in energy metabolism together with the occurrence of enzymes of central metabolism in the nucleus gave rise to the active research field aiming to understand moonlighting enzymes that undergo post-translational modifications before carrying out new tasks. Recent Advances Cytosolic enzymes were shown to induce gene transcription after post-translational modification and concomitant translocation to the nucleus. Changed properties of the oxidized forms of cytosolic glyceraldehyde 3-phosphate dehydrogenase (GAPDH), but also malate dehydrogenases and others, are the basis for a hypothesis suggesting moonlighting functions that directly link energy metabolism to adaptive responses required for maintenance of redox-homeostasis in all eukaryotes. Critical Issues Small molecules, such as metabolic intermediates, coenzymes, or reduced glutathione, were shown to fine-tune the redox-switches, interlinking redox-state, metabolism, and induction of new functions via nuclear gene expression. The cytosol with its metabolic enzymes connecting energy fluxes between the various cell compartments can be seen as a hub for redox-signaling, integrating the different signals for graded and directed responses in stressful situations. Future directions Enzymes of central metabolism were shown to interact with p53 or the assumed plant homolog SOG1 (suppressor of gamma response 1), a NAC transcription factor involved in the stress response upon UV exposure. Metabolic enzymes serve as sensors for imbalances, their inhibition leading to changed energy metabolism, and the adoption of transcriptional co-activator activities. Depending on the intensity of the impact, re-routing of energy metabolism, proliferation, DNA repair, cell cycle arrest, immune responses, or cell death will be induced.
    DOI:  https://doi.org/10.1089/ars.2020.8121
  36. Front Oncol. 2020 ;10 928
    Yamaguchi H, Taouk GM.
      Yes-Associated Protein (YAP) and Transcriptional Co-activator with PDZ-binding Motif (TAZ) are the downstream effectors of the Hippo signaling pathway that play a crucial role in various aspects of cancer progression including metastasis. Metastasis is the multistep process of disseminating cancer cells in a body and responsible for the majority of cancer-related death. Emerging evidence has shown that cancer cells reprogram their metabolism to gain proliferation, invasion, migration, and anti-apoptotic abilities and adapt to various environment during metastasis. Moreover, it has increasingly been recognized that YAP/TAZ regulates cellular metabolism that is associated with the phenotypic changes, and recent studies suggest that the YAP/TAZ-mediated metabolic alterations contribute to metastasis. In this review, we will introduce the latest knowledge of YAP/TAZ regulation and function in cancer metastasis and metabolism, and discuss possible links between the YAP/TAZ-mediated metabolic reprogramming and metastasis.
    Keywords:  TAZ; YAP; cancer; metabolism; metastasis
    DOI:  https://doi.org/10.3389/fonc.2020.00928
  37. Nat Commun. 2020 Jul 03. 11(1): 3301
    Ye K, Meng WX, Sun H, Wu B, Chen M, Pang YP, Gao J, Wang H, Wang J, Kaufmann SH, Dai H.
      Many cellular stresses are transduced into apoptotic signals through modification or up-regulation of the BH3-only subfamily of BCL2 proteins. Through direct or indirect mechanisms, these proteins activate BAK and BAX to permeabilize the mitochondrial outer membrane. While the BH3-only proteins BIM, PUMA, and tBID have been confirmed to directly activate BAK through its canonical BH3 binding groove, whether the BH3-only proteins BMF, HRK or BIK can directly activate BAK is less clear. Here we show that BMF and HRK bind and directly activate BAK. Through NMR studies, site-directed mutagenesis, and advanced molecular dynamics simulations, we also find that BAK activation by BMF and possibly HRK involves a previously unrecognized binding groove formed by BAK α4, α6, and α7 helices. Alterations in this groove decrease the ability of BMF and HRK to bind BAK, permeabilize membranes and induce apoptosis, suggesting a potential role for this BH3-binding site in BAK activation.
    DOI:  https://doi.org/10.1038/s41467-020-17074-y
  38. Cell. 2020 Jun 23. pii: S0092-8674(20)30693-0. [Epub ahead of print]
    Wu CC, Peterson A, Zinshteyn B, Regot S, Green R.
      Problems arising during translation of mRNAs lead to ribosome stalling and collisions that trigger a series of quality control events. However, the global cellular response to ribosome collisions has not been explored. Here, we uncover a function for ribosome collisions in signal transduction. Using translation elongation inhibitors and general cellular stress conditions, including amino acid starvation and UV irradiation, we show that ribosome collisions activate the stress-activated protein kinase (SAPK) and GCN2-mediated stress response pathways. We show that the MAPKKK ZAK functions as the sentinel for ribosome collisions and is required for immediate early activation of both SAPK (p38/JNK) and GCN2 signaling pathways. Selective ribosome profiling and biochemistry demonstrate that although ZAK generally associates with elongating ribosomes on polysomal mRNAs, it specifically auto-phosphorylates on the minimal unit of colliding ribosomes, the disome. Together, these results provide molecular insights into how perturbation of translational homeostasis regulates cell fate.
    Keywords:  SAPK; UV radiation; ZAK; amino acid starvation; integrated stress response; ribosome collisions
    DOI:  https://doi.org/10.1016/j.cell.2020.06.006
  39. Annu Rev Cell Dev Biol. 2020 Jun 30.
    Marshall WF.
      As cells grow, the size and number of their internal organelles increase in order to keep up with increased metabolic requirements. Abnormal size of organelles is a hallmark of cancer and an important aspect of diagnosis in cytopathology. Most organelles vary in either size or number, or both, as a function of cell size, but the mechanisms that create this variation remain unclear. In some cases, organelle size appears to scale with cell size through processes of relative growth, but in others the size may be set by either active measurement systems or genetic programs that instruct organelle biosynthetic activities to create organelles of a size appropriate to a given cell type. Expected final online publication date for the Annual Review of Cell and Developmental Biology, Volume 36 is October 6, 2020. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    DOI:  https://doi.org/10.1146/annurev-cellbio-020520-113246
  40. FEBS Lett. 2020 Jul 03.
    Kreuzer M, Banerjee A, Birts CN, Darley M, Tavassoli A, Ivan M, Blaydes JP.
      Adaptive responses to hypoxia are mediated by the hypoxia-inducible factor (HIF) family of transcription factors. These responses include the upregulation of glycolysis to maintain ATP production. This also generates acidic metabolites, which require HIF-induced carbonic anhydrase IX (CAIX) for their neutralisation. C-terminal binding proteins (CtBPs) are co-regulators of gene transcription and couple glycolysis with gene transcription due to their regulation by the glycolytic coenzyme NADH. Here, we find that experimental manipulation of glycolysis and CtBP function in breast cancer cells through multiple complementary approaches supports a hypothesis whereby the expression of known HIF-inducible genes, and CAIX in particular, adapts to available glucose in the microenvironment through a mechanism involving CtBPs. This novel pathway promotes the survival of stem cell-like cancer (SCLC) cells in hypoxia.
    Keywords:  Hypoxia; NADH; breast cancer; carbonic anhydrase IX; glycolysis; stem cell-like cancer cells
    DOI:  https://doi.org/10.1002/1873-3468.13874