bims-camemi 2018-12-30 papers

bims-camemi

Biomed News

on Mitochondrial metabolism in cancer

Issue of 2018‒12‒30
34 papers selected by
Christian Frezza,

Role of Mitochondria in Ferroptosis.
The impact of exercise on mitochondrial dynamics and the role of Drp1 in exercise performance and training adaptations in skeletal muscle.
Mitochondrial quality orchestrates muscle-adipose dialog to alleviate dietary obesity.
Transglutaminase Type 2 Regulates ER-Mitochondria Contact Sites by Interacting with GRP75.
Clinical Practice Guidance: Surveillance for phaeochromocytoma and paraganglioma in paediatric succinate dehydrogenase gene mutation carriers.
Clinical and Biochemical Features in a Patient With Mitochondrial Fission Factor Gene Alteration.
Drp1-Zip1 Interaction Regulates Mitochondrial Quality Surveillance System.
The dependence of brain mitochondria reactive oxygen species production on oxygen level is linear, except when inhibited by antimycin A.
A mitochondrial FUNDC1/HSC70 interaction organizes the proteostatic stress response at the risk of cell morbidity.
Super-resolution microscopy localizes perilipin 5 at lipid droplet-mitochondria interaction sites and at lipid droplets juxtaposing to perilipin 2.
The Interface Between ER and Mitochondria: Molecular Compositions and Functions.
Temporal dynamics of liver mitochondrial protein acetylation and succinylation and metabolites due to high fat diet and/or excess glucose or fructose.
Targeting mitochondrial quality control for treating sarcopenia: lessons from physical exercise.
Low metformin causes a more oxidized mitochondrial NADH/NAD redox state in hepatocytes and inhibits gluconeogenesis by a redox-independent mechanism.
The single mitochondrion of the kinetoplastid parasite Crithidia fasciculata is a dynamic network.
Assessing the fitness consequences of mitonuclear interactions in natural populations.
Stressing out the mitochondria: Mechanistic insights into NLRP3 inflammasome activation.
Regulation of acetate metabolism and coordination with the TCA cycle via a processed small RNA.
Increased Mitochondrial Protein Levels and Bioenergetics in the Musculus Rectus Femoris of Wfs1-Deficient Mice.
Mitochondrial lysine deacetylation promotes energy metabolism and calcium signaling in insulin-secreting cells.
A specific lipid metabolic profile is associated with the epithelial mesenchymal transition program.
Glycolytic Switch Is Required for Transdifferentiation to Endothelial Lineage.
p53 Represses the Mevalonate Pathway to Mediate Tumor Suppression.
Mitochondria modulate programmed neuritic retraction.
VHL Dependent Expression of REDD1 and PDK3 Proteins in Clear-cell Renal Cell Carcinoma.
Mitochondrial aquaporin-8 is involved in SREBP-controlled hepatocyte cholesterol biosynthesis.
RNA G-quadruplexes at upstream open reading frames cause DHX36- and DHX9-dependent translation of human mRNAs.
Structural and Biochemical Characterization of Aldehyde Dehydrogenase 12, the Last Enzyme of Proline Catabolism in Plants.
Starvation and Pseudo-Starvation as Drivers of Cancer Metastasis through Translation Reprogramming.
Lactate Dehydrogenase C Is Required for the Protein Expression of a Sperm-specific Isoform of Lactate Dehydrogenase A.
TFEB controls vascular development by regulating the proliferation of endothelial cells.
Identification of Novel Protein Targets of Dimethyl Fumarate Modification in Neurons and Astrocytes Reveals Actions Independent of Nrf2 Stabilization.
Lipidomic profiling reveals early-stage metabolic dysfunction in overweight or obese humans.
The Role of Succinate in the Regulation of Intestinal Inflammation.

Mol Cell. 2018 Dec 13. pii: S1097-2765(18)30936-5. [Epub ahead of print]

Role of Mitochondria in Ferroptosis.

Minghui Gao, Junmei Yi, Jiajun Zhu, Alexander M Minikes, Prashant Monian, Craig B Thompson, Xuejun Jiang.

Ferroptosis is a regulated necrosis process driven by iron-dependent lipid peroxidation. Although ferroptosis and cellular metabolism interplay with one another, whether mitochondria are involved in ferroptosis is under debate. Here, we demonstrate that mitochondria play a crucial role in cysteine-deprivation-induced ferroptosis but not in that induced by inhibiting glutathione peroxidase-4 (GPX4), the most downstream component of the ferroptosis pathway. Mechanistically, cysteine deprivation leads to mitochondrial membrane potential hyperpolarization and lipid peroxide accumulation. Inhibition of mitochondrial TCA cycle or electron transfer chain (ETC) mitigated mitochondrial membrane potential hyperpolarization, lipid peroxide accumulation, and ferroptosis. Blockage of glutaminolysis had the same inhibitory effect, which was counteracted by supplying downstream TCA cycle intermediates. Importantly, loss of function of fumarate hydratase, a tumor suppressor and TCA cycle component, confers resistance to cysteine-deprivation-induced ferroptosis. Collectively, this work demonstrates the crucial role of mitochondria in cysteine-deprivation-induced ferroptosis and implicates ferroptosis in tumor suppression.

DOI: https://doi.org/10.1016/j.molcel.2018.10.042
Mol Metab. 2018 Dec 04. pii: S2212-8778(18)30786-5. [Epub ahead of print]

The impact of exercise on mitochondrial dynamics and the role of Drp1 in exercise performance and training adaptations in skeletal muscle.

Timothy M Moore, Zhenqi Zhou, Whitaker Cohn, Frode Norheim, Amanda J Lin, Nareg Kalajian, Alexander R Strumwasser, Kevin Cory, Kate Whitney, Theodore Ho, Timothy Ho, Joseph L Lee, Daniel H Rucker, Orian Shirihai, Alexander M van der Bliek, Julian P Whitelegge, Marcus M Seldin, Aldons J Lusis, Sindre Lee, Christian A Drevon, Sushil K Mahata, Lorraine P Turcotte, Andrea L Hevener.

  OBJECTIVE: Mitochondria are organelles primarily responsible for energy production, and recent evidence indicates that alterations in size, shape, location, and quantity occur in response to fluctuations in energy supply and demand. We tested the impact of acute and chronic exercise on mitochondrial dynamics signaling and determined the impact of the mitochondrial fission regulator Dynamin related protein (Drp)1 on exercise performance and muscle adaptations to training.METHODS: Wildtype and muscle-specific Drp1 heterozygote (mDrp1+/-) mice, as well as dysglycemic (DG) and healthy normoglycemic men (control) performed acute and chronic exercise. The Hybrid Mouse Diversity Panel, including 100 murine strains of recombinant inbred mice, was used to identify muscle Dnm1L (encodes Drp1)-gene relationships.
RESULTS: Endurance exercise impacted all aspects of the mitochondrial life cycle, i.e. fission-fusion, biogenesis, and mitophagy. Dnm1L gene expression and Drp1Ser616 phosphorylation were markedly increased by acute exercise and declined to baseline during post-exercise recovery. Dnm1L expression was strongly associated with transcripts known to regulate mitochondrial metabolism and adaptations to exercise. Exercise increased the expression of DNM1L in skeletal muscle of healthy control and DG subjects, despite a 15% ↓(P = 0.01) in muscle DNM1L expression in DG at baseline. To interrogate the role of Dnm1L further, we exercise trained male mDrp1+/- mice and found that Drp1 deficiency reduced muscle endurance and running performance, and altered muscle adaptations in response to exercise training.
CONCLUSION: Our findings highlight the importance of mitochondrial dynamics, specifically Drp1 signaling, in the regulation of exercise performance and adaptations to endurance exercise training.

Keywords:  Drp1; Exercise performance; Exercise training; Mitochondrial dynamics

DOI:  https://doi.org/10.1016/j.molmet.2018.11.012
Pharmacol Res. 2018 Dec 21. pii: S1043-6618(18)31478-6. [Epub ahead of print]

Mitochondrial quality orchestrates muscle-adipose dialog to alleviate dietary obesity.

Zhisheng Xu, Tingting Fu, Qiqi Guo, Wanping Sun, Zhenji Gan.

  Skeletal muscle fitness is vital for human health and disease and is determined by the capacity for burning fuel, mitochondrial ATP production, and contraction. High quality mitochondria in skeletal muscle are essential for maintaining energy homeostasis in response to a myriad of physiologic or pathophysiological stresses. A sophisticated mitochondrial quality control system including mitochondrial autophagy, dynamics, and proteolysis has been identified, which maintains their functional integrity. In this review, we discuss recent studies highlighting mitochondrial quality control mechanisms that govern systemic metabolism by skeletal muscles. Increasing evidence suggests that mitochondria can "communicate" with the nucleus and triggers adaptive genomic re-programming during stress response. We focus on participation of the mitochondrial quality control system in the regulation of mitochondrial communications that drive the muscle to adipose dialog and suggest that muscle-specific regulation of mitochondrial quality impacts systemic homeostasis.

Keywords:  adaptive thermogenesis; adipose; metabolic homeostasis; mitochondrial quality control; muscle

DOI:  https://doi.org/10.1016/j.phrs.2018.12.020
Cell Rep. 2018 Dec 26. pii: S2211-1247(18)31885-0. [Epub ahead of print]25(13): 3573-3581.e4

Transglutaminase Type 2 Regulates ER-Mitochondria Contact Sites by Interacting with GRP75.

Manuela D'Eletto, Federica Rossin, Luca Occhigrossi, Maria Grazia Farrace, Danilo Faccenda, Radha Desai, Saverio Marchi, Giulia Refolo, Laura Falasca, Manuela Antonioli, Fabiola Ciccosanti, Gian Maria Fimia, Paolo Pinton, Michelangelo Campanella, Mauro Piacentini.

  Transglutaminase type 2 (TG2) is a multifunctional enzyme that plays a key role in mitochondria homeostasis under stressful cellular conditions. TG2 interactome analysis reveals an enzyme interaction with GRP75 (glucose-regulated protein 75). GRP75 localizes in mitochondria-associated membranes (MAMs) and acts as a bridging molecule between the two organelles by assembling the IP3R-GRP75-VDAC complex, which is involved in the transport of Ca2+ from the endoplasmic reticulum (ER) to mitochondria. We demonstrate that the TG2 and GRP75 interaction occurs in MAMs. The absence of the TG2-GRP75 interaction leads to an increase of the interaction between IP3R-3 and GRP75; a decrease of the number of ER-mitochondria contact sites; an impairment of the ER-mitochondrial Ca2+ flux; and an altered profile of the MAM proteome. These findings indicate TG2 is a key regulatory element of the MAMs.

Keywords:  ER-mitochondria contact sites; GRP75; MAMs; TG2; mitochondrial Ca(2+)

DOI:  https://doi.org/10.1016/j.celrep.2018.11.094
Clin Endocrinol (Oxf). 2018 Dec 27.

Clinical Practice Guidance: Surveillance for phaeochromocytoma and paraganglioma in paediatric succinate dehydrogenase gene mutation carriers.

Mei Yin Wong, Katrina A Andrews, Benjamin G Challis, Soo-Mi Park, Carlo L Acerini, Eamonn R Maher, Ruth T Casey.

The Succinate dehydrogenase (SDH) enzyme complex functions as a key enzyme coupling the oxidation of succinate to fumarate in the citric acid cycle. Inactivation of this enzyme complex results in the cellular accumulation of the oncometabolite succinate, which is postulated to be a key driver in tumourigenesis. Succinate accumulation inhibits 2-oxoglutarate-dependent dioxygenases, including DNA and histone demethylase enzymes and hypoxic gene response regulators. Biallelic inactivation (typically resulting from one inherited and one somatic event) at one of the four genes encoding the SDH complex (SDHA/B/C/D), is the most common cause for SDH deficient (dSDH) tumours. Germline mutations in the SDHx genes predispose to a spectrum of tumours including phaeochromocytoma and paraganglioma (PPGL), wild type gastrointestinal stromal tumours (wtGIST) and, less commonly, renal cell carcinoma and pituitary tumours (1). Furthermore, mutations in the SDHx genes, particularly SDHB, predispose to a higher risk of malignant PPGL, which is associated with a five year mortality of 50% (2). There is general agreement that biochemical and imaging surveillance should be offered to asymptomatic carriers of SDHx gene mutations in the expectation that this will reduce the morbidity and mortality associated with dSDH tumours (3). However, there is no consensus on when and how surveillance should be performed in children and young adults. Here, we address the question: 'What age should clinical, biochemical and radiological surveillance for PPGL be initiated in paediatric SDHx mutation carriers? This article is protected by copyright. All rights reserved.

DOI: https://doi.org/10.1111/cen.13926
Front Genet. 2018 ;9 625

Clinical and Biochemical Features in a Patient With Mitochondrial Fission Factor Gene Alteration.

Alessia Nasca, Francesca Nardecchia, Anna Commone, Michela Semeraro, Andrea Legati, Barbara Garavaglia, Daniele Ghezzi, Vincenzo Leuzzi.

  Mitochondrial Fission Factor (MFF) is part of a protein complex that promotes mitochondria and peroxisome fission. Hitherto, only 5 patients have been reported harboring mutations in MFF, all of them with the clinical features of a very early onset Leigh-like encephalopathy. We report on an 11-year-old boy with epileptic encephalopathy. He presented with neurological regression, epileptic myoclonic seizures, severe intellectual disability, microcephaly, tetraparesis, optic atrophy, and ophthalmoplegia. Brain MRI pattern was compatible with Leigh syndrome. NGS-based analysis of a gene panel for mitochondrial disorders revealed a homozygous c.892C>T (p. Arg298*) in the MFF gene. Fluorescence staining detected abnormal morphology of mitochondria and peroxisomes in fibroblasts from the patient; a strong reduction in MFF protein levels and the presence of truncated forms were observed. No biochemical alterations denoting peroxisomal disorders were found. As reported in other disorders affecting the dynamics of intracellular organelles, our patient showed clinical features suggesting both mitochondrial and peroxisomal impairment. High levels of lactate in our case suggested an involvement of the energetic metabolism but without clear respiratory chain deficiency, while biomarkers of peroxisomal dysfunction were normal. We confirm that MFF mutations are associated with epileptic encephalopathy with Leigh-like MRI pattern.

Keywords:  MFF; epileptic encephalopathy; leigh syndrome; mitochondria; mitochondrial disorders; mitochondrial fission factor; peroxisome

DOI:  https://doi.org/10.3389/fgene.2018.00625
Mol Cell. 2018 Dec 01. pii: S1097-2765(18)30979-1. [Epub ahead of print]

Drp1-Zip1 Interaction Regulates Mitochondrial Quality Surveillance System.

Hyo Min Cho, Jae Ryun Ryu, Youhwa Jo, Tae Woong Seo, Ye Na Choi, June Hoan Kim, Jee Min Chung, Bongki Cho, Ho Chul Kang, Seong-Woon Yu, Soon Ji Yoo, Hyun Kim, Woong Sun.

  Mitophagy, a mitochondrial quality control process for eliminating dysfunctional mitochondria, can be induced by a response of dynamin-related protein 1 (Drp1) to a reduction in mitochondrial membrane potential (MMP) and mitochondrial division. However, the coordination between MMP and mitochondrial division for selecting the damaged portion of the mitochondrial network is less understood. Here, we found that MMP is reduced focally at a fission site by the Drp1 recruitment, which is initiated by the interaction of Drp1 with mitochondrial zinc transporter Zip1 and Zn2+ entry through the Zip1-MCU complex. After division, healthy mitochondria restore MMP levels and participate in the fusion-fission cycle again, but mitochondria that fail to restore MMP undergo mitophagy. Thus, interfering with the interaction between Drp1 and Zip1 blocks the reduction of MMP and the subsequent mitophagic selection of damaged mitochondria. These results suggest that Drp1-dependent fission provides selective pressure for eliminating "bad sectors" in the mitochondrial network, serving as a mitochondrial quality surveillance system.

Keywords:  Drp1; Zip1; mitochondrial fission; mitochondrial membrane potential; mitochondrial quality control; mitochondrial quality surveillance; mitophagy

DOI:  https://doi.org/10.1016/j.molcel.2018.11.009
J Neurochem. 2018 Dec 24.

The dependence of brain mitochondria reactive oxygen species production on oxygen level is linear, except when inhibited by antimycin A.

Anna Stepanova, Csaba Konrad, Giovanni Manfredi, Roger Springett, Vadim Ten, Alexander Galkin.

  Reactive oxygen species (ROS) are byproducts of physiological mitochondrial metabolism that are involved in several cellular signaling pathways as well as tissue injury and pathophysiological processes, including brain ischemia-reperfusion injury. The mitochondrial respiratory chain is considered a major source of ROS; however, there is little agreement on how ROS release depends on oxygen concentration. The rate of H2 O2 release by intact brain mitochondria was measured with an Amplex UltraRed assay using a high-resolution respirometer (Oroboros) equipped with a fluorescent optical module and a system of controlled gas flow for varying the oxygen concentration. Three types of substrates were used: malate and pyruvate, succinate and glutamate, succinate alone or glycerol 3-phosphate. For the first time we determined that, with any substrate used in the absence of inhibitors, H2 O2 release by respiring brain mitochondria is linearly dependent on the oxygen concentration. We found that the highest rate of H2 O2 release occurs in conditions of reverse electron transfer when mitochondria oxidize succinate or glycerol 3-phosphate. H2 O2 production by complex III is significant only in the presence of antimycin A and, in this case, the oxygen dependence manifested mixed (linear and hyperbolic) kinetics. We also demonstrated that complex II in brain mitochondria could contribute to ROS generation even in the absence of its substrate succinate when the quinone pool is reduced by glycerol 3-phosphate. Our results underscore the critical importance of reverse electron transfer in the brain, where a significant amount of succinate can be accumulated during ischemia providing a backflow of electrons to complex I at the early stages of reperfusion. Our study also demonstrates that ROS generation in brain mitochondria is lower under hypoxic conditions than in normoxia. This article is protected by copyright. All rights reserved.

Keywords:  ROS generation; antimycin A; complex I; ischemia-reperfusion; mitochondria; reverse electron transfer

DOI:  https://doi.org/10.1111/jnc.14654
EMBO J. 2018 Dec 27. pii: e98786. [Epub ahead of print]

A mitochondrial FUNDC1/HSC70 interaction organizes the proteostatic stress response at the risk of cell morbidity.

Yanjun Li, Yanhong Xue, Xiaojun Xu, Guopeng Wang, Yiqun Liu, Hao Wu, Wenhui Li, Yueying Wang, Ziheng Chen, Weilin Zhang, Yushan Zhu, Wei Ji, Tao Xu, Lei Liu, Quan Chen.

  Both protein quality and mitochondrial quality are vital for the cellular activity, and impaired proteostasis and mitochondrial dysfunction are common etiologies of aging and age-related disorders. Here, we report that the mitochondrial outer membrane protein FUNDC1 interacts with the chaperone HSC70 to promote the mitochondrial translocation of unfolded cytosolic proteins for degradation by LONP1 or for formation of non-aggresomal mitochondrion-associated protein aggregates (MAPAs) upon proteasome inhibition in cultured human cells. Integrative approaches including csCLEM, Apex, and biochemical analysis reveal that MAPAs contain ubiquitinated cytosolic proteins, autophagy receptor p62, and mitochondrial proteins. MAPAs are segregated from mitochondria in a FIS1-dependent manner and can subsequently be degraded via autophagy. Although the FUNDC1/HSC70 pathway promotes the degradation of unfolded cytosolic proteins, excessive accumulation of unfolded proteins on the mitochondria prior to MAPA formation impairs mitochondrial integrity and activates AMPK, leading to cellular senescence. We suggest that human mitochondria organize cellular proteostatic response at the risk of their own malfunction and cell lethality.

Keywords:  cellular senescence; mitochondria; mitochondrial quality control; mitophagy; proteostatic stress

DOI:  https://doi.org/10.15252/embj.201798786
Biochim Biophys Acta Mol Cell Biol Lipids. 2018 Nov;pii: S1388-1981(18)30257-9. [Epub ahead of print]1863(11): 1423-1432

Super-resolution microscopy localizes perilipin 5 at lipid droplet-mitochondria interaction sites and at lipid droplets juxtaposing to perilipin 2.

Anne Gemmink, Sabine Daemen, Helma J H Kuijpers, Gert Schaart, Hans Duimel, Carmen López-Iglesias, Marc A M J van Zandvoort, Kèvin Knoops, Matthijs K C Hesselink.

  OBJECTIVE: Intramyocellular lipid droplets (LD) and their coat proteins PLIN2 and PLIN5 are involved in lipolysis, with a putative role for PLIN5 in mitochondrial tethering. Reportedly, these proteins co-localize and cover the surface of the LD. To provide the spatial basis for understanding how these proteins possess their distinct roles, we examined the precise location of PLIN2 and PLIN5 and explored PLIN5 presence at LD-mitochondria contact sites using Stimulated emission depletion (STED) microscopy and correlative light-electron microscopy (CLEM) in human skeletal muscle sections.METHODS: LDs were stained by MDH together with combinations of mitochondrial proteins and PLINs. Subcellular distribution and co-localization of PLIN proteins and mitochondria was imaged by STED microscopy (Leica TCS SP8) and quantified using Pearson's correlation coefficients and intensity profile plots. CLEM was employed to examine the presence of PLIN5 on mitochondria-LD contact sites.
RESULTS: Both PLIN2 and PLIN5 localized to the LD in a dot-like, juxtaposed fashion rather than colocalizing and covering the entire LD. Both STED and CLEM revealed a high fraction of PLIN5 at the LD-mitochondria interface, but not at mitochondrial cristae, as suggested previously.
CONCLUSION: Using two super-resolution imaging approaches, this is the first study to show that in sections of human skeletal muscle PLIN2 and PLIN5 localize to the LD at distinct sites, with abundance of PLIN5 at LD-mitochondria tethering sites. This novel spatial information uncovers that PLIN proteins do not serve as lipolytic barriers but rather are docking sites for proteins facilitating selective lipase access under a variety of lipolytic conditions.

Keywords:  Lipid droplets; Mitochondria; Perilipin 2; Perilipin 5; Skeletal muscle; Super-resolution microscopy

DOI:  https://doi.org/10.1016/j.bbalip.2018.08.016
Mol Cells. 2018 Dec 31. 41(12): 1000-1007

The Interface Between ER and Mitochondria: Molecular Compositions and Functions.

Soyeon Lee, Kyung-Tai Min.

  Mitochondria and endoplasmic reticulum (ER) are essential organelles in eukaryotic cells, which play key roles in various biological pathways. Mitochondria are responsible for ATP production, maintenance of Ca2+ homeostasis and regulation of apoptosis, while ER is involved in protein folding, lipid metabolism as well as Ca2+ homeostasis. These organelles have their own functions, but they also communicate via mitochondrial-associated ER membrane (MAM) to provide another level of regulations in energy production, lipid process, Ca2+ buffering, and apoptosis. Hence, defects in MAM alter cell survival and death. Here, we review components forming the molecular junctions of MAM and how MAM regulates cellular functions. Furthermore, we discuss the effects of impaired ER-mitochondrial communication in various neurodegenerative diseases.

Keywords:  ER-mitochondria tethering; mitochondrial-associated ER membrane (MAM); neurodegenerative disease

DOI:  https://doi.org/10.14348/molcells.2018.0438
PLoS One. 2018 ;13(12): e0208973

Temporal dynamics of liver mitochondrial protein acetylation and succinylation and metabolites due to high fat diet and/or excess glucose or fructose.

Jesse G Meyer, Samir Softic, Nathan Basisty, Matthew J Rardin, Eric Verdin, Bradford W Gibson, Olga Ilkayeva, Christopher B Newgard, C Ronald Kahn, Birgit Schilling.

Dietary macronutrient composition alters metabolism through several mechanisms, including post-translational modification (PTM) of proteins. To connect diet and molecular changes, here we performed short- and long-term feeding of mice with standard chow diet (SCD) and high-fat diet (HFD), with or without glucose or fructose supplementation, and quantified liver metabolites, 861 proteins, and 1,815 protein level-corrected mitochondrial acetylation and succinylation sites. Nearly half the acylation sites were altered by at least one diet; nutrient-specific changes in protein acylation sometimes encompass entire pathways. Although acetyl-CoA is an intermediate in both sugar and fat metabolism, acetyl-CoA had a dichotomous fate depending on its source; chronic feeding of dietary sugars induced protein hyperacetylation, whereas the same duration of HFD did not. Instead, HFD resulted in citrate accumulation, anaplerotic metabolism of amino acids, and protein hypo-succinylation. Together, our results demonstrate novel connections between dietary macronutrients, protein post-translational modifications, and regulation of fuel selection in liver.

DOI: https://doi.org/10.1371/journal.pone.0208973
Expert Opin Ther Targets. 2018 Dec 22. 1-8

Targeting mitochondrial quality control for treating sarcopenia: lessons from physical exercise.

Anna Picca, Riccardo Calvani, Christiaan Leeuwenburgh, Hélio José Coelho-Junior, Roberto Bernabei, Francesco Landi, Emanuele Marzetti.

  INTRODUCTION: Mitochondrial dysfunction is a hallmark of aging and hence is a candidate target for intervention. Sarcopenia of aging is a prevalent condition and is associated with numerous negative health outcomes. Alterations in mitochondrial homeostasis have been reported in sarcopenic muscle. Area covered: We discuss the evidence that points to mitochondrial dysfunction having a causative role in sarcopenia and the mechanisms involved in the accumulation of damaged mitochondria in the aged muscle. We also discuss the effects of physical exercise on mitochondrial quality control and muscle health in advanced age. Expert opinion: In the aged muscle, the mitochondrial quality control axis is altered at several levels, including proteostasis, biogenesis, dynamics, and autophagy. Mitochondrial dysfunction arising from impaired quality control is thought to play a major role in the pathogenesis of sarcopenia. Physical exercise is the most effective strategy for the management of sarcopenia. Improvements in mitochondrial health and plasticity may mediate several beneficial effects of exercise in muscle. A greater understanding of the molecular changes that occur in the aged muscle following exercise and how they impact mitochondrial homeostasis is necessary for the exploration of potential targets that are amenable for interventions.

Keywords:  autophagy; mitochondrial biogenesis; mitochondrial dynamics; mitochondrial proteostasis; mitophagy; physical activity; physical exercise; resistance training

DOI:  https://doi.org/10.1080/14728222.2019.1559827
J Biol Chem. 2018 Dec 27. pii: jbc.RA118.006670. [Epub ahead of print]

Low metformin causes a more oxidized mitochondrial NADH/NAD redox state in hepatocytes and inhibits gluconeogenesis by a redox-independent mechanism.

Ahmed Alshawi, Loranne Agius.

  The mechanisms by which metformin (dimethylbiguanide) inhibits hepatic gluconeogenesis at concentrations relevant for type 2 diabetes therapy remain debated. Two proposed mechanisms are: inhibition of mitochondrial Complex 1 with consequent compromised ATP and AMP homeostasis; or inhibition of mitochondrial glycerophosphate dehydrogenase (mGPDH) and thereby attenuated transfer of reducing equivalents from the cytoplasm to mitochondria resulting in a raised lactate/pyruvate ratio and redox-dependent inhibition of gluconeogenesis from reduced but not oxidised substrates. Here we show that metformin has a biphasic effect on the mitochondrial NADH/NAD redox state in mouse hepatocytes. A low cell dose of metformin (therapeutic equivalent: < 2nmol / mg) caused a more oxidized mitochondrial NADH/NAD state and an increase in lactate / pyruvate ratio, whereas a higher metformin dose (³5nmol/mg) caused a more reduced mitochondrial NADH/NAD state similar to Complex 1 inhibition by rotenone. The low metformin dose inhibited gluconeogenesis from both oxidized (dihydroxyacetone) and reduced (xylitol) substrates by preferential partitioning of substrate towards glycolysis by a redox-independent mechanism that is best explained by allosteric regulation at phosphor-fructokinase-1 (PFK1) and/or fructose bisphosphatase-1 (FBP-1) in association with a decrease in cell glycerol 3-P, an inhibitor of PFK1 rather than by inhibition of transfer of reducing equivalents. We conclude that at a low pharmacological load, the metformin effects on the lactate / pyruvate ratio and glucose production are explained by attenuation of transmitochondrial electrogenic transport mechanisms with consequent compromised malate-aspartate shuttle and changes in allosteric effectors of PFK1 and FBP1.

Keywords:  gluconeogenesis; metabolic disease; metabolic regulation; metformin; redox regulation

DOI:  https://doi.org/10.1074/jbc.RA118.006670
PLoS One. 2018 ;13(12): e0202711

The single mitochondrion of the kinetoplastid parasite Crithidia fasciculata is a dynamic network.

John DiMaio, Gordon Ruthel, Joshua J Cannon, Madeline F Malfara, Megan L Povelones.

Mitochondria are central organelles in cellular metabolism. Their structure is highly dynamic, allowing them to adapt to different energy requirements, to be partitioned during cell division, and to maintain functionality. Mitochondrial dynamics, including membrane fusion and fission reactions, are well studied in yeast and mammals but it is not known if these processes are conserved throughout eukaryotic evolution. Kinetoplastid parasites are some of the earliest-diverging eukaryotes to retain a mitochondrion. Each cell has only a single mitochondrial organelle, making them an interesting model for the role of dynamics in controlling mitochondrial architecture. We have investigated the mitochondrial division cycle in the kinetoplastid Crithidia fasciculata. The majority of mitochondrial biogenesis occurs during the G1 phase of the cell cycle, and the mitochondrion is divided symmetrically in a process coincident with cytokinesis. Live cell imaging revealed that the mitochondrion is highly dynamic, with frequent changes in the topology of the branched network. These remodeling reactions include tubule fission, fusion, and sliding, as well as new tubule formation. We hypothesize that the function of this dynamic remodeling is to homogenize mitochondrial contents and to facilitate rapid transport of mitochondria-encoded gene products from the area containing the mitochondrial nucleoid to other parts of the organelle.

DOI: https://doi.org/10.1371/journal.pone.0202711
Biol Rev Camb Philos Soc. 2018 Dec 26.

Assessing the fitness consequences of mitonuclear interactions in natural populations.

Geoffrey E Hill, Justin C Havird, Daniel B Sloan, Ronald S Burton, Chris Greening, Damian K Dowling.

  Metazoans exist only with a continuous and rich supply of chemical energy from oxidative phosphorylation in mitochondria. The oxidative phosphorylation machinery that mediates energy conservation is encoded by both mitochondrial and nuclear genes, and hence the products of these two genomes must interact closely to achieve coordinated function of core respiratory processes. It follows that selection for efficient respiration will lead to selection for compatible combinations of mitochondrial and nuclear genotypes, and this should facilitate coadaptation between mitochondrial and nuclear genomes (mitonuclear coadaptation). Herein, we outline the modes by which mitochondrial and nuclear genomes may coevolve within natural populations, and we discuss the implications of mitonuclear coadaptation for diverse fields of study in the biological sciences. We identify five themes in the study of mitonuclear interactions that provide a roadmap for both ecological and biomedical studies seeking to measure the contribution of intergenomic coadaptation to the evolution of natural populations. We also explore the wider implications of the fitness consequences of mitonuclear interactions, focusing on central debates within the fields of ecology and biomedicine.

Keywords:  coadaptation; coevolution; epistatic interactions; fitness; gene flow; mitochondria; mitochondrial medicine; speciation

DOI:  https://doi.org/10.1111/brv.12493
J Leukoc Biol. 2018 Dec 27.

Stressing out the mitochondria: Mechanistic insights into NLRP3 inflammasome activation.

Monica Yabal, Dale J Calleja, Daniel S Simpson, Kate E Lawlor.

  Inflammasomes are multimeric protein complexes that induce the cleavage and release of bioactive IL-1β and cause a lytic form of cell death, termed pyroptosis. Due to its diverse triggers, ranging from infectious pathogens and host danger molecules to environmental irritants, the NOD-like receptor protein 3 (NLRP3) inflammasome remains the most widely studied inflammasome to date. Despite intense scrutiny, a universal mechanism for its activation remains elusive, although, recent research has focused on mitochondrial dysfunction or potassium (K+ ) efflux as key events. In this review, we give a general overview of NLRP3 inflammasome activation and explore the recently emerging noncanonical and alternative pathways to NLRP3 activation. We highlight the role of the NLRP3 inflammasome in the pathogenesis of metabolic disease that is associated with mitochondrial and oxidative stress. Finally, we interrogate the mechanisms proposed to trigger NLRP3 inflammasome assembly and activation. A greater understanding of how NLRP3 inflammasome activation is triggered may reveal new therapeutic targets for the treatment of inflammatory disease.

Keywords:  caspases; inflammasome; metabolism; mitochondria; reactive oxygen species

DOI:  https://doi.org/10.1002/JLB.MR0318-124R
Proc Natl Acad Sci U S A. 2018 Dec 27. pii: 201815288. [Epub ahead of print]

Regulation of acetate metabolism and coordination with the TCA cycle via a processed small RNA.

François De Mets, Laurence Van Melderen, Susan Gottesman.

  Bacterial regulatory small RNAs act as crucial regulators in central carbon metabolism by modulating translation initiation and degradation of target mRNAs in metabolic pathways. Here, we demonstrate that a noncoding small RNA, SdhX, is produced by RNase E-dependent processing from the 3'UTR of the sdhCDAB-sucABCD operon, encoding enzymes of the tricarboxylic acid (TCA) cycle. In Escherichia coli, SdhX negatively regulates ackA, which encodes an enzyme critical for degradation of the signaling molecule acetyl phosphate, while the downstream pta gene, encoding the enzyme critical for acetyl phosphate synthesis, is not significantly affected. This discoordinate regulation of pta and ackA increases the accumulation of acetyl phosphate when SdhX is expressed. Mutations in sdhX that abolish regulation of ackA lead to more acetate in the medium (more overflow metabolism), as well as a strong growth defect in the presence of acetate as sole carbon source, when the AckA-Pta pathway runs in reverse. SdhX overproduction confers resistance to hydroxyurea, via regulation of ackA SdhX abundance is tightly coupled to the transcription signals of TCA cycle genes but escapes all known posttranscriptional regulation. Therefore, SdhX expression directly correlates with transcriptional input to the TCA cycle, providing an effective mechanism for the cell to link the TCA cycle with acetate metabolism pathways.

Keywords:  Hfq; RybD; acetate kinase; acetyl-phosphate; hydroxyurea

DOI:  https://doi.org/10.1073/pnas.1815288116
Oxid Med Cell Longev. 2018 ;2018 3175313

Increased Mitochondrial Protein Levels and Bioenergetics in the Musculus Rectus Femoris of Wfs1-Deficient Mice.

Margus Eimre, Kalju Paju, Nadežda Peet, Lumme Kadaja, Marian Tarrend, Sergo Kasvandik, Joosep Seppet, Marilin Ivask, Ehte Orlova, Sulev Kõks.

Wfs1 deficiency leads to a progressive loss of plasma insulin concentration, which should reduce the consumption of glucose in insulin-dependent tissues, causing a variety of changes in intracellular energy metabolism. Our objective here was to assess the changes in the amount and function of mitochondrial proteins in different muscles of Wfs1-deficient mice. Mitochondrial functions were assayed by high-resolution oxygraphy of permeabilized muscle fibers; the protein amount was evaluated by liquid chromatography tandem mass spectrometry (LC/MS/MS) analysis and mRNA levels of the uncoupler proteins UCP2 and UCP3 by real-time PCR; and citrate synthase (CS) activity was determined spectrophotometrically in muscle homogenates. Compared to controls, there were no changes in proton leak and citrate synthase activity in the heart and m. soleus tissues of Wfs1-deficient mice, but significantly higher levels of both of these factors were observed in the m. rectus femoris; mitochondrial proteins and mRNA of UCP2 were also higher in the m. rectus femoris. ADP-stimulated state 3 respiration was lower in the m. soleus, remained unchanged in the heart, and was higher in the m. rectus femoris. The mitochondrial protein amount and activity are higher in Wfs1-deficient mice, as are mitochondrial proton leak and oxygen consumption in m. rectus femoris. These changes in muscle metabolism may be important for identifying the mechanisms responsible for Wolfram syndrome and diabetes.

DOI: https://doi.org/10.1155/2018/3175313
FASEB J. 2018 Dec 27. fj201801424R

Mitochondrial lysine deacetylation promotes energy metabolism and calcium signaling in insulin-secreting cells.

Umberto De Marchi, Antonio Núñez Galindo, Jonathan Thevenet, Aurélie Hermant, Flavien Bermont, Steve Lassueur, Jaime Santo Domingo, Martin Kussmann, Loïc Dayon, Andreas Wiederkehr.

  In pancreatic β-cells, mitochondria generate signals that promote insulin granule exocytosis. Here we study how lysine acetylation of mitochondrial proteins mechanistically affects metabolism-secretion coupling in insulin-secreting cells. Using mass spectrometry-based proteomics, we identified lysine acetylation sites in rat insulinoma cell line clone 1E cells. In cells lacking the mitochondrial lysine deacetylase sirtuin-3 (SIRT3), several matrix proteins are hyperacetylated. Disruption of the SIRT3 gene has a deleterious effect on mitochondrial energy metabolism and Ca2+ signaling. Under resting conditions, SIRT3 deficient cells are overactivated, which elevates the respiratory rate and enhances calcium signaling and basal insulin secretion. In response to glucose, the SIRT3 knockout cells are unable to mount a sustained cytosolic ATP response. Calcium signaling is strongly reduced and the respiratory response as well as insulin secretion are blunted. We propose mitochondrial protein lysine acetylation as a control mechanism in β-cell energy metabolism and Ca2+ signaling.-De Marchi, U., Galindo, A. N., Thevenet, J., Hermant, A., Bermont, F., Lassueur, S., Domingo, J. S., Kussmann, M., Dayon, L., Wiederkehr, A. Mitochondrial lysine deacetylation promotes energy metabolism and calcium signaling in insulin-secreting cells.

Keywords:  SIRT3; mitochondria; pancreatic; type 2 diabetes; β-cells

DOI:  https://doi.org/10.1096/fj.201801424R
Biochim Biophys Acta Mol Cell Biol Lipids. 2018 Dec 19. pii: S1388-1981(18)30374-3. [Epub ahead of print]

A specific lipid metabolic profile is associated with the epithelial mesenchymal transition program.

Anna Maria Giudetti, Stefania De Domenico, Andrea Ragusa, Paola Lunetti, Antonio Gaballo, Julien Franck, Pasquale Simeone, Giuseppe Nicolardi, Francesco De Nuccio, Angelo Santino, Loredana Capobianco, Paola Lanuti, Isabelle Fournier, Michel Salzet, Michele Maffia, Daniele Vergara.

  Several studies have identified a specific metabolic program that is associated with the process of epithelial-mesenchymal transition (EMT). Whereas much is known about the association between glucose metabolism and EMT, the contribution of lipid metabolism is not still completely understood. Here, we studied epithelial and mesenchymal breast cancer cells by proteomic and lipidomic approaches and identified significant differences that characterised these models concerning specific metabolic enzymes and metabolites including fatty acids and phospholipids. Higher levels of monounsaturated fatty acids together with increased expression of enzymes of de novo fatty acid synthesis is the distinct signature of epithelial with respect to mesenchymal cells that, on the contrary, show reduced lipogenesis, higher polyunsaturated fatty acids level and increased expression of genes involved in the triglyceride (TAG) synthesis and lipid droplets formation. In the mesenchymal model, the diacylglycerol acyltransferase (DGAT)-1 appears to be the major enzyme involved in TAG synthesis and inhibition of DGAT1, but not DGAT2, drastically reduces the incorporation of labeled palmitate into TAG. Moreover, knockdown of β-catenin demonstrated that this metabolic phenotype in under the control of a network of transcriptional factors and that β-catenin has a specific role in the regulation of lipid metabolism in mesenchymal cells.

Keywords:  Epithelial mesenchymal transition; Lipids; Mass spectrometry; Metabolism; β-Catenin

DOI:  https://doi.org/10.1016/j.bbalip.2018.12.011
Circulation. 2019 Jan 02. 139(1): 119-133

Glycolytic Switch Is Required for Transdifferentiation to Endothelial Lineage.

Li Lai, Erin Reineke, Dale J Hamilton, John P Cooke.

  BACKGROUND: We have previously shown that activation of cell-autonomous innate immune signaling facilitates the transdifferentiation of fibroblasts into induced endothelial cells, and is required to generate induced endothelial cells with high fidelity for endothelial lineage. Recent studies indicate that a glycolytic switch plays a role in induced pluripotent stem cell generation from somatic cells.METHODS: Seahorse and metabolomics flux assays were used to measure the metabolic changes during transdifferentiation in vitro, and Matrigel plug assay was used to assess the effects of glycolysis modulators on transdifferentiation in vivo.
RESULTS: The metabolic switch begins rapidly after activation of innate immunity, before the expression of markers of endothelial lineage. Inhibiting glycolysis impaired, whereas facilitating glycolysis enhanced, the generation of induced endothelial cells. The toll-like receptor 3 agonist poly I:C increased expression of the mitochondrial citrate transporter Slc25A1, and the nuclear ATP-citrate lyase, in association with intracellular accumulation of citrate, the precursor for acetyl coenzyme A. These metabolic changes were coordinated with increased histone acetylation during transdifferentiation.
CONCLUSION: Innate immune signaling promotes a glycolytic switch that is required for transdifferentiation, both processes being attenuated by ATP-citrate lyase knockdown. These data shed light on a novel link between metabolism and epigenetic modulation in transdifferentiation.

Keywords:  cell transdifferentiation; endothelium; glycolysis; mitochondria

DOI:  https://doi.org/10.1161/CIRCULATIONAHA.118.035741
Cell. 2018 Dec 14. pii: S0092-8674(18)31503-4. [Epub ahead of print]

p53 Represses the Mevalonate Pathway to Mediate Tumor Suppression.

Sung-Hwan Moon, Chun-Hao Huang, Shauna L Houlihan, Kausik Regunath, William A Freed-Pastor, John P Morris, Darjus F Tschaharganeh, Edward R Kastenhuber, Anthony M Barsotti, Rachel Culp-Hill, Wen Xue, Yu-Jui Ho, Timour Baslan, Xiang Li, Allison Mayle, Elisa de Stanchina, Lars Zender, David R Tong, Angelo D'Alessandro, Scott W Lowe, Carol Prives.

  There are still gaps in our understanding of the complex processes by which p53 suppresses tumorigenesis. Here we describe a novel role for p53 in suppressing the mevalonate pathway, which is responsible for biosynthesis of cholesterol and nonsterol isoprenoids. p53 blocks activation of SREBP-2, the master transcriptional regulator of this pathway, by transcriptionally inducing the ABCA1 cholesterol transporter gene. A mouse model of liver cancer reveals that downregulation of mevalonate pathway gene expression by p53 occurs in premalignant hepatocytes, when p53 is needed to actively suppress tumorigenesis. Furthermore, pharmacological or RNAi inhibition of the mevalonate pathway restricts the development of murine hepatocellular carcinomas driven by p53 loss. Like p53 loss, ablation of ABCA1 promotes murine liver tumorigenesis and is associated with increased SREBP-2 maturation. Our findings demonstrate that repression of the mevalonate pathway is a crucial component of p53-mediated liver tumor suppression and outline the mechanism by which this occurs.

Keywords:  ABCA1; SREBP-2; cancer metabolism; mevalonate pathway; p53; tumor suppression

DOI:  https://doi.org/10.1016/j.cell.2018.11.011
Proc Natl Acad Sci U S A. 2018 Dec 24. pii: 201811021. [Epub ahead of print]

Mitochondria modulate programmed neuritic retraction.

Sergei V Baranov, Oxana V Baranova, Svitlana Yablonska, Yalikun Suofu, Alberto L Vazquez, Takashi D Y Kozai, X Tracy Cui, Lisa M Ferrando, Timothy M Larkin, Yulia Y Tyurina, Valerian E Kagan, Diane L Carlisle, Bruce S Kristal, Robert M Friedlander.

  Neuritic retraction in the absence of overt neuronal death is a shared feature of normal aging and neurodegenerative disorders, but the intracellular mechanisms modulating this process are not understood. We propose that cumulative distal mitochondrial protein damage results in impaired protein import, leading to mitochondrial dysfunction and focal activation of the canonical apoptosis pathway in neurites. This is a controlled process that may not lead to neuronal death and, thus, we term this phenomenon "neuritosis." Consistent with our hypothesis, we show that in primary cerebrocortical neurons, mitochondrial distance from the soma correlates with increased mitochondrial protein damage, PINK1 accumulation, reactive oxygen species production, and decreased mitochondrial membrane potential and depolarization threshold. Furthermore, we demonstrate that the distance-dependent mitochondrial membrane potential gradient exists in vivo in mice. We demonstrate that impaired distal mitochondria have a lower threshold for focal/nonlethal neuritic caspase-3 activation in normal neurons that is exacerbated in aging, stress, and neurodegenerative conditions, thus delineating a fundamental mechanistic underpinning for synaptic vulnerability.

Keywords:  caspase-3; mitochondrial membrane potential; mutant huntingtin; neurite retraction; neurodegeneration

DOI:  https://doi.org/10.1073/pnas.1811021116
J Med Biochem. 2018 Jan;37(1): 31-38

VHL Dependent Expression of REDD1 and PDK3 Proteins in Clear-cell Renal Cell Carcinoma.

Bojana B Ilic, Jadranka A Antic, Jovana Z Bankovic, Ivana T Milicevic, Gordana S Rodic, Dusan S Ilic, Cane D Tulic, Vera N Todorovic, Svetozar S Damjanovic.

  Background: Sporadic clear-cell renal cell carcinoma (ccRCC) is associated with mutations in the VHL gene, upregulated mammalian target of rapamycin (mTOR) activity and glycolytic metabolism. Here, we analyze the effect of VHL mutational status on the expression level of mTOR, eIF4E-BP1, AMPK, REDD1, and PDK3 proteins.Methods: Total proteins were isolated from 21 tumorous samples with biallelic inactivation, 10 with monoallelic inactivation and 6 tumors with a wild-type VHL (wtVHL) gene obtained from patients who underwent total nephrectomy. The expressions of target proteins were assessed using Western blot.
Results: Expressions of mTOR, eIF4EBP1 and AMPK were VHL independent. Tumors with monoallelic inactivation of VHL underexpressed REDD1 in comparison to wtVHL tumors (P = 0.042), tumors with biallelic VHL inactivation (P < 0.005) and control tissue (P = 0.004). Additionally, REDD1 expression was higher in tumors with VHL biallelic inactivation than in control tissue (P = 0.008). Only in wt tumor samples PDK3 was overexpressed in comparison to tumors with biallelic inactivation of VHL gene (P = 0.012) and controls (P = 0.016). In wtVHL ccRCC, multivariate linear regression analysis revealed that 97.4% of variability in PDK3 expression can be explained by variations in AMPK amount.
Conclusion: Expressions of mTOR, eIF4EBP1 and AMPK were VHL independent. We have shown for the first time VHL dependent expression of PDK3 and we provide additional evidence that VHL mutational status affects REDD1 expression in sporadic ccRCC.

Keywords:  VHL gene; clear-cell renal cell carcinoma; mammalian target of rapamycin; pyruvate dehydrogenase kinase 3; regulated in development and DNA damage responses

DOI:  https://doi.org/10.1515/jomb-2017-0030
Free Radic Biol Med. 2018 Dec 20. pii: S0891-5849(18)31065-7. [Epub ahead of print]

Mitochondrial aquaporin-8 is involved in SREBP-controlled hepatocyte cholesterol biosynthesis.

Mauro Danielli, Julieta Marrone, Alejo M Capiglioni, Raúl A Marinelli.

  Cholesterol, via sterol regulatory element-binding protein (SREBP) transcription factors, activates or represses genes involved in its hepatic biosynthetic pathway, and also modulates the expression of hepatocyte mitochondrial aquaporin-8 (mtAQP8), a channel that can function as peroxiporin by facilitating the transmembrane diffusion of H2O2. Here we tested the hypothesis that mtAQP8 is involved in the SREBP-mediated regulation of hepatocyte cholesterol biosynthesis. Using human hepatocyte-derived Huh-7 cells and primary rat hepatocytes, we found that mtAQP8 knockdown significantly downregulated de novo cholesterol synthesis as well as protein expressions of SREBP-2 and its target gene, the rate-limiting enzyme in cholesterol synthesis 3-Hydroxy-3-Methylglutaryl-CoA Reductase (HMGCR). In contrast, adenovirus-mediated human AQP8 mitochondrial expression significantly increased de novo cholesterol synthesis and protein expressions of SREBP-2 and HMGCR. In mtAQP8-overexpressed cells, mitochondrial H2O2 release was found to be increased, and a mitochondria-targeted antioxidant prevented the upregulation of hepatocyte cholesterol synthesis. Our results suggest that peroxiporin mtAQP8 plays a role in the SREBP-controlled hepatocyte cholesterogenesis, a finding that might be relevant to cholesterol-related metabolic disorders.

Keywords:  aquaporin-8; cholesterogenesis; hepatocytes; mitochondrial H(2)O(2)

DOI:  https://doi.org/10.1016/j.freeradbiomed.2018.12.016
Genome Biol. 2018 Dec 27. 19(1): 229

RNA G-quadruplexes at upstream open reading frames cause DHX36- and DHX9-dependent translation of human mRNAs.

Pierre Murat, Giovanni Marsico, Barbara Herdy, Avazeh Ghanbarian, Guillem Portella, Shankar Balasubramanian.

  BACKGROUND: RNA secondary structures in the 5'-untranslated regions (5'-UTR) of mRNAs are key to the post-transcriptional regulation of gene expression. While it is evident that non-canonical Hoogsteen-paired G-quadruplex (rG4) structures somehow contribute to the regulation of translation initiation, the nature and extent of human mRNAs that are regulated by rG4s is not known. Here, we provide new insights into a mechanism by which rG4 formation modulates translation.RESULTS: Using transcriptome-wide ribosome profiling, we identify rG4-driven mRNAs in HeLa cells and reveal that rG4s in the 5'-UTRs of inefficiently translated mRNAs associate with high ribosome density and the translation of repressive upstream open reading frames (uORF). We demonstrate that depletion of the rG4-unwinding helicases DHX36 and DHX9 promotes translation of rG4-associated uORFs while reducing the translation of coding regions for transcripts that comprise proto-oncogenes, transcription factors and epigenetic regulators. Transcriptome-wide identification of DHX9 binding sites shows that reduced translation is mediated through direct physical interaction between the helicase and its rG4 substrate.
CONCLUSION: This study identifies human mRNAs whose translation efficiency is modulated by the DHX36- and DHX9-dependent folding/unfolding of rG4s within their 5'-UTRs. We reveal a previously unknown mechanism for translation regulation in which unresolved rG4s within 5'-UTRs promote 80S ribosome formation on upstream start codons, causing inhibition of translation of the downstream main open reading frames. Our findings suggest that the interaction of helicases with rG4s could be targeted for future therapeutic intervention.

Keywords:  G-quadruplexes; Helicases; RNA secondary structures; Translation regulation; Upstream open reading frames

DOI:  https://doi.org/10.1186/s13059-018-1602-2
J Mol Biol. 2018 Dec 20. pii: S0022-2836(18)31047-7. [Epub ahead of print]

Structural and Biochemical Characterization of Aldehyde Dehydrogenase 12, the Last Enzyme of Proline Catabolism in Plants.

David A Korasick, Radka Končitíková, Martina Kopečná, Eva Hájková, Armelle Vigouroux, Solange Moréra, Donald F Becker, Marek Šebela, John J Tanner, David Kopečný.

  Heterokonts, Alveolata protists, green algae from Charophyta and Chlorophyta divisions, and all Embryophyta plants possess an aldehyde dehydrogenase (ALDH) gene named ALDH12. Here, we provide a biochemical characterization of two ALDH12 family members from the lower plant Physcomitrella patens and higher plant Zea mays. We show ALDH12 encodes an NAD+-dependent glutamate γ-semialdehyde dehydrogenase (GSALDH), which irreversibly converts glutamate γ-semialdehyde (GSAL), a mitochondrial intermediate of the proline and arginine catabolism, to glutamate. Sedimentation equilibrium and small-angle X-ray scattering analyses reveal that in solution both plant GSALDHs exist as equilibrium between a domain-swapped dimer and the dimer-of-dimers tetramer. Plant GSALDHs share very low sequence identity with bacterial, fungal, and animal GSALDHs (classified as ALDH4), which are the closest related ALDH superfamily members. Nevertheless, the crystal structure of ZmALDH12 at 2.2 Å resolution shows that nearly all key residues involved in the recognition of GSAL are identical to those in ALDH4, indicating a close functional relationship with ALDH4. Phylogenetic analysis suggests that the transition from ALDH4 to ALDH12 occurred during the evolution of the endosymbiotic plant ancestor, prior to the evolution of green algae and land plants. Finally, ALDH12 expression in maize and moss is downregulated in response to salt and drought stresses, possibly to maintain proline levels. Taken together, these results provide molecular insight into the biological roles of the plant ALDH12 family.

Keywords:  ALDH12; Aldehyde dehydrogenase; Gene expression; Glutamate γ-semialdehyde; Physcomitrella patens; Proline; Site-directed mutagenesis; X-ray crystallography; Zea mays

DOI:  https://doi.org/10.1016/j.jmb.2018.12.010
Cell Metab. 2018 Dec 13. pii: S1550-4131(18)30737-X. [Epub ahead of print]

Starvation and Pseudo-Starvation as Drivers of Cancer Metastasis through Translation Reprogramming.

Custodia García-Jiménez, Colin R Goding.

  Considerable progress has been made in identifying microenvironmental signals that effect the reversible phenotypic transitions underpinning the early steps in the metastatic cascade. However, although the general principles underlying metastatic dissemination have been broadly outlined, a common theme that unifies many of the triggers of invasive behavior in tumors has yet to emerge. Here we discuss how many diverse signals that induce invasion converge on the reprogramming of protein translation via phosphorylation of eIF2α, a hallmark of the starvation response. These include starvation as a consequence of nutrient or oxygen limitation, or pseudo-starvation imposed by cell-extrinsic microenvironmental signals or by cell-intrinsic events, including oncogene activation. Since in response to resource limitation single-cell organisms undergo phenotypic transitions remarkably similar to those observed within tumors, we propose that a starvation/pseudo-starvation model to explain cancer progression provides an integrated and evolutionarily conserved conceptual framework to understand the progression of this complex disease.

Keywords:  cancer heterogeneity; eIF2α; invasion; nutrient supply and demand; phenotypic plasticity; pseudo-starvation; translation reprogramming

DOI:  https://doi.org/10.1016/j.cmet.2018.11.018
J Biochem. 2018 Dec 24.

Lactate Dehydrogenase C Is Required for the Protein Expression of a Sperm-specific Isoform of Lactate Dehydrogenase A.

Mina Dodo, Hiroshi Kitamura, Hiroki Shima, Daisuke Saigusa, Sisca Meida Wati, Nao Ota, Fumiki Katsuoka, Hatsune Chiba, Hiroaki Okae, Takahiro Arima, Kazuhiko Igarashi, Takeyoshi Koseki, Hiroki Sekine, Hozumi Motohashi.

Metabolites are sensitive indicators of moment-to-moment cellular status and activity. Expecting that tissue-specific metabolic signatures unveil a unique function of the tissue, we examined metabolomes of mouse liver and testis and found that an unusual metabolite, 2-hydroxyglutarate (2-HG), was abundantly accumulated in the testis. 2-HG can exist as D- or L-enantiomer, and both enantiomers interfere with the activities of 2-oxoglutarate (2-OG)-dependent dioxygenases, such as the Jumonji family of histone demethylases. Whereas D-2-HG is produced by oncogenic mutants of isocitrate dehydrogenases (IDH) and known as an oncometabolite, L-2-HG was the major enantiomer detected in the testis, suggesting that a distinct mechanism underlies the testicular production of this metabolite. We clarified that lactate dehydrogenase C (LDHC), a testis-specific lactate dehydrogenase, is responsible for L-2-HG accumulation by generating and analyzing Ldhc-deficient mice. Although the inhibitory effects of 2-HG on 2-OG-dependent dioxygenases were barely observed in the testis, the LDHA protein level was remarkably decreased in Ldhc-deficient sperm, indicating that LDHC is required for LDHA expression in the sperm. This unique functional interaction between LDH family members supports lactate dehydrogenase activity in the sperm. The severely impaired motility of Ldhc-deficient sperm suggests a substantial contribution of glycolysis to energy production for sperm motility.

DOI: https://doi.org/10.1093/jb/mvy108
EMBO J. 2018 Dec 27. pii: e98250. [Epub ahead of print]

TFEB controls vascular development by regulating the proliferation of endothelial cells.

Gabriella Doronzo, Elena Astanina, Davide Corà, Giulia Chiabotto, Valentina Comunanza, Alessio Noghero, Francesco Neri, Alberto Puliafito, Luca Primo, Carmine Spampanato, Carmine Settembre, Andrea Ballabio, Giovanni Camussi, Salvatore Oliviero, Federico Bussolino.

  Transcription factor TFEB is thought to control cellular functions-including in the vascular bed-primarily via regulation of lysosomal biogenesis and autophagic flux. Here, we report that TFEB also orchestrates a non-canonical program that controls the cell cycle/VEGFR2 pathway in the developing vasculature. In endothelial cells, TFEB depletion halts proliferation at the G1-S transition by inhibiting the CDK4/Rb pathway. TFEB-deficient cells attempt to compensate for this limitation by increasing VEGFR2 levels at the plasma membrane via microRNA-mediated mechanisms and controlled membrane trafficking. TFEB stimulates expression of the miR-15a/16-1 cluster, which limits VEGFR2 transcript stability and negatively modulates expression of MYO1C, a regulator of VEGFR2 trafficking to the cell surface. Altered levels of miR-15a/16-1 and MYO1C in TFEB-depleted cells cause increased expression of plasma membrane VEGFR2, but in a manner associated with low signaling strength. An endothelium-specific Tfeb-knockout mouse model displays defects in fetal and newborn mouse vasculature caused by reduced endothelial proliferation and by anomalous function of the VEGFR2 pathway. These previously unrecognized functions of TFEB expand its role beyond regulation of the autophagic pathway in the vascular system.

Keywords:  angiogenesis; embryo; membrane trafficking; miRNA transcription; proliferation

DOI:  https://doi.org/10.15252/embj.201798250
Mol Cell Proteomics. 2018 Dec 26. pii: mcp.RA118.000922. [Epub ahead of print]

Identification of Novel Protein Targets of Dimethyl Fumarate Modification in Neurons and Astrocytes Reveals Actions Independent of Nrf2 Stabilization.

Gerardo G Piroli, Allison M Manuel, Tulsi Patel, Michael D Walla, Liang Shi, Scott A Lanci, Jingtian Wang, Ashley Galloway, Pavel I Ortinski, Deanna S Smith, Norma Frizzell.

  The fumarate ester dimethyl fumarate (DMF) has been introduced recently as a treatment for relapsing remitting multiple sclerosis (RRMS), a chronic inflammatory condition that results in neuronal demyelination and axonal loss. DMF is known to act by depleting intracellular glutathione and modifying thiols on Keap1 protein, resulting in the stabilization of the transcription factor Nrf2, which in turn induces the expression of antioxidant response element genes. We have previously shown that DMF reacts with a wide range of protein thiols, suggesting that the complete mechanisms of action of DMF are unknown. Here, we investigated other intracellular thiol residues that may also be irreversibly modified by DMF in neurons and astrocytes. Using mass spectrometry, we identified 24 novel proteins that were modified by DMF in neurons and astrocytes, including cofilin-1, tubulin and collapsin response mediator protein 2 (CRMP2). Using an in vitro functional assay, we demonstrated that DMF-modified cofilin-1 loses its activity and generates less monomeric actin, potentially inhibiting its cytoskeletal remodeling activity, which could be beneficial in the modulation of myelination during RRMS. DMF modification of tubulin did not significantly impact axonal lysosomal trafficking. We found that the oxygen consumption rate of N1E-115 neurons and the levels of proteins related to mitochondrial energy production were only slightly affected by the highest doses of DMF, confirming that DMF treatment does not impair cellular respiratory function. In summary, our work provides new insights into the mechanisms supporting the neuroprotective and re-myelination benefits associated with DMF treatment in addition to the antioxidant response by Nrf2.

Keywords:  Chemical biology; Dimethyl fumarate; Drug targets*; Mechanism of action; Post-translational modifications*; Protein adducts; Succination

DOI:  https://doi.org/10.1074/mcp.RA118.000922
Biochim Biophys Acta Mol Cell Biol Lipids. 2018 Dec 23. pii: S1388-1981(18)30242-7. [Epub ahead of print]

Lipidomic profiling reveals early-stage metabolic dysfunction in overweight or obese humans.

Aya Mousa, Negar Naderpoor, Natalie Mellett, Kirsty Wilson, Magdalena Plebanski, Peter J Meikle, Barbora de Courten.

  BACKGROUND: Advances in mass spectrometry and lipidomics techniques are providing new insights into the role of lipid metabolism in obesity-related diseases. However, human lipidomic studies have been inconsistent, owing to the use of indirect proxy measures of metabolic outcomes and relatively limited coverage of the lipidome. Here, we employed comprehensive lipid profiling and gold-standard metabolic measures to test the hypothesis that distinct lipid signatures in obesity may signify early stages of pathogenesis toward type 2 diabetes.METHODS: Using high-performance liquid chromatography-electrospray tandem mass spectrometry, we profiled >450 lipid species across 26 classes in 65 overweight or obese non-diabetic individuals. Intensive metabolic testing was conducted using direct gold-standard measures of adiposity (% body fat by dual X-ray absorptiometry), insulin sensitivity (hyperinsulinaemic-euglycaemic clamps), and insulin secretion (intravenous glucose tolerance tests), as well as measurement of serum inflammatory cytokines and adipokines (multiplex assays; flow cytometry). Univariable and multivariable linear regression models were computed using Matlab R2011a, and all analyses were corrected for multiple testing using the Benjamini-Hochberg method.
RESULTS: We present new evidence showing a strong and independent positive correlation between the lysophosphatidylinositol (LPI) lipid class and insulin secretion in vivo in humans (β [95% CI] = 781.9 [353.3, 1210.4], p = 0.01), supporting the insulinotropic effects of LPI demonstrated in mouse islets. Dihydroceramide, a sphingolipid precursor, was independently and negatively correlated with insulin sensitivity (β [95% CI] = -1.9 [-2.9, -0.9], p = 0.01), indicating a possible upregulation in sphingolipid synthesis in obese individuals. These associations remained significant in multivariable models adjusted for age, sex, and % body fat. The dihexosylceramide class correlated positively with interleukin-10 before and after adjustment for age, sex, and % body fat (p = 0.02), while the phosphatidylethanolamine class and its vinyl ether-linked (plasmalogen) derivatives correlated negatively with % body fat in both univariable and age- and sex-adjusted models (all p < 0.04).
CONCLUSIONS: Our data suggest that these lipid classes may signify early pathogenesis toward type 2 diabetes and could serve as novel therapeutic targets or biomarkers for diabetes prevention.

Keywords:  Diabetes; Insulin secretion; Lipid metabolism; Lipidomics; Metabolic dysfunction; Obesity

DOI:  https://doi.org/10.1016/j.bbalip.2018.12.014
Nutrients. 2018 Dec 22. pii: E25. [Epub ahead of print]11(1):

The Role of Succinate in the Regulation of Intestinal Inflammation.

Jessica Connors, Nick Dawe, Johan Van Limbergen.

  Succinate is a metabolic intermediate of the tricarboxylic acid (TCA) cycle within host cells. Succinate is also produced in large amounts during bacterial fermentation of dietary fiber. Elevated succinate levels within the gut lumen have been reported in association with microbiome disturbances (dysbiosis), as well as in patients with inflammatory bowel disease (IBD) and animal models of intestinal inflammation. Recent studies indicate that succinate can activate immune cells via its specific surface receptor, succinate receptor 1(SUCNR1), and enhance inflammation. However, the role of succinate in inflammatory processes within the gut mucosal immune system is unclear. This review includes current literature on the association of succinate with intestinal inflammation and the potential role of succinate⁻SUCNR1 signaling in gut immune functions.

Keywords:  dysbiosis; inflammatory bowel disease; metabolic receptor; metabolite; microbiome

DOI:  https://doi.org/10.3390/nu11010025