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Research > Team Cell Energetic Metabolism

Cell Energetic Metabolism

Principal Investigator : Anne Devin

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Team Members

Antonin André - Doctorant visiteur

Nicole Avéret - MCU UB

Cyrielle Bouchez - Doctorante MESR

Sylvain Cuvellier - AI CNRS

Anne Devin - DR2 CNRS

Stephane Duvezin-Caubet - CRCN CNRS

Louise Injarabian - Doctorante MESR

Benoit Marteyn - Visiteur CR1 INSERM

Jean-Pierre Mazat - Professeur émérite UB

Patrick Paumard - MCU UB

Stéphane Ransac - MCU UB

Michel Rigoulet - Professeur émérite UB

 

Former Team Members

Pascal Baret - Invited MCU (2010-2011) Mariam Marsan - Post-doc (2006-2008)
Cyrille Chevtzoff - MESR PhD (2005-2008) Arnaud Mourier - MESR PhD (2005-2008)
Edgar D Yoboue – MESR PhD (2008-2011) Damien Quinton – Post-doc (2013-2014)
Rodrigo Diaz-Ruiz - co-supervised PhD Mexique (2010)

 

Summary

Cell energy metabolism includes energy conversion that leads to NADH reoxydation and ATP production. Two cellular pathways are involved in these processes: glycolysis and oxidative phosphorylation. Our laboratory is primarily involved in studying the control and regulation of oxidative phosphorylation during cell proliferation. Indeed the cellular needs for both ATP synthesis and NADH reoxydation are susceptible to huge variations with rapid kinetics and this requires tight adjustments from the cell. We thus study the mechanisms that allow such adjustments. This is achieved at three levels of integration: the cellular level, the isolated mitochondria level and the oxidative phosphorylation complexes level. Our main cellular model is the yeast Saccharomyces cerevisiae which, when grown on non-fermentable substrate has a respiratory obligatory growth.

 

Research Activity

A - Control and regulation of cell energy metabolism at the cellular level

The question that was addressed was to identify how, during growth, cell ATP synthesis adjusted to ATP demand. Indeed, there are two ways, which are not exclusive, to do so: (i) a kinetic regulation of the activity of the respiratory chain and (ii) the modulation of the number of respiratory chain subunits that can function at the same rate. Assessing the amount of mitochondria (by means of quantifying mitochondrial cytochromes) and their functioning within cells during growth allowed us to show that cell energy metabolism was modulated through variations in the amount of mitochondria with a constant respiratory rate steady state. Moreover, we were able to show that the signaling pathway involved in the regulation of the amount of mitochondria was the cAMP pathway. Yeast cells harbor 3 cAMP protein kinase isoforms (Tpk1-2-3) and we showed that Tpk3 was the isoform involved in the process of interest. In the absence of Tpk3, mitochondria produce more reactive oxygen species –ROS- (due to tpk3-cAMP induced decrease in ROS production), and these ROS signal to the mitochondrial biogenesis transcriptional coactivator HAP4p that is then degraded, which decreases mitochondrial biogenesis. In conclusion, we showed that (i) cell energy metabolism during growth is adjusted by means of mitochondrial biogenesis (ii) mitochondrial ROS are involved in mitochondria to nucleus signaling, allowing a mitochondria quality control process.

In aerobiosis, glycolysis and oxidative phosphorylation are coordinated in order to satisfy the cell energy demand. In numerous cell types, glucose addition to the culture medium induces an inhibition of respiration. This metabolic adaptation was first observed by HG Crabtree in 1929 and is since then known as the Crabtree effect. This respiration inhibition has profound metabolic consequences (glycolysis becomes the privileged energetic pathway) that lead to a deregulation of cell proliferation and its origin has long been studied. Even though there are numerous hypotheses concerning its origin, no consensual mechanism exists to this day. We have recently shown that Fructose 16bisphosphate, a glycolysis intermediate, plays a key role in this respiration inhibition that is central in metabolic rearrangements observed in cancer cells. The Crabtree effect induces an important remodeling of cell energy metabolism that can ultimately lead to the Warburg effect (important repression of mitochondrial metabolism) that has been shown in numerous cancer cells. On the basis of our previous results we study the relationships between the Crabtree and the Warburg effects and the molecular mechanisms that are set up upon the Crabtree effect induction.

 

B - Control and regulation of cell energy metabolism at the isolated mitochondria level

Studies conducted on isolated mitochondria are usually done in the presence of a single respiratory substrate. However, in the cytosol, mitochondria are in the presence of multiple substrates at the same time. We thus studied, on mitochondria isolated from the yeast Saccharomyces cerevisiae, substrates reoxydation when several substrates are present. Yeast mitochondria respiratory chain harbors a number of dehydrogenases that give their electrons to the quinone pool. Electrons are then transferred to proton pumping complex III and IV that allow the establishment of the proton motive force, which will be used for ATP synthesis. Our study showed that external NADH dehydrogenase isoform Nde1 has the right of way for electrons transfer on the other dehydrogenases. Moreover, using a ?CRD1 strain that does not synthesize cardiolipids –essential for the supramolecular organization of the respiratory chain- we showed that this supramolecular organization of the respiratory chain is not involved in the electrons priority process from NADH dehydrogenase. Thanks to the integration to our group of JP Mazat and S Ransac, who elaborated a model of the mitochondrial respiratory chain, we were able to show that this electron competition process is due to the enzymes kinetic properties. Indeed, experiments aiming to determine the enzymes kinetics properties were integrated in their model and exhibited a nice fit.

In conclusion, we showed that cytosolic NADH reoxydation is favored in yeast mitochondria when in presence of multiple substrates and that this is due to the kinetic properties of the enzymes. This is physiologically sound since during growth there is a positive net synthesis of NADH, whose reoxydation is mandatory in order to maintain growth.

 

C - Studying oxidative phosphorylation complexes: a stochastic approach

The realization of multiple mitochondrial functions is dependent on a large number of simultaneous interactions. It renders its analysis difficult and certainly non-intuitive. For this reason mathematical modeling is of great help in understanding all these interactions and their phenotypical consequences. The stochastic approach of electron transfers in respiratory chain complexes and super complexes is a typical example for using a model to integrate a set of results obtained with different methods in order to understand a complex behaviour. Indeed, a stochastic approach is particularly well adapted to describe the time course of the redox reactions that occur inside the respiratory chain complexes. Accordingly, we approached the molecular functioning of the bc1 complex (complex III) based on its known crystallographic structure and the midpoint potential of redox centers. The main features of our simulations are the dominant and robust emergence of a Q-cycle mechanism and the near absence of by-passes in the normal functioning of the bc1 complex. We also use this approach to describe the molecular functioning of the hydrophilic domain of complex I. This allows simulating the kinetic behaviour of a population of this complex as it occurs in a spectrophotometer cuvet and to successively compare our experimental data to the model simulations based on different physico-chemical properties.

 

Keywords

Mitochondria - Metabolism - Energy metabolism - Metabolism rewiring - Crabtree effect - Warburg effect - Modeling

 

Selected publications 2009-2018

Rosas Lemus M, Roussarie E, Hammad N, Mougeolle A, Ransac S, Issa R, Mazat JP, Uribe-Carvajal S, Rigoulet M, Devin A. The role of glycolysis-derived hexose phosphates in the induction of the Crabtree effect. J Biol Chem. 2018 Aug 17;293(33):12843-12854

Baret P, Le Sage F, Planesse C, Meilhac O, Devin A, Bourdon E, Rondeau P. Glycated human albumin alters mitochondrial respiration in preadipocyte 3T3-L1 cells. Biofactors. 2017 Jul 8;43(4):577-592

Charles E, Hammadi M, Kischel P, Delcroix V, Demaurex N, Castelbou C, Vacher AM, Devin A, Ducret T, Nunes P, Vacher P. The antidepressant fluoxetine induces necrosis by energy depletion and mitochondrial calcium overload. Oncotarget. 2017 Jan 10;8(2):3181-3196

Colombié S, Beauvoit B, Nazaret C, Bénard C, Vercambre G, Le Gall S, Biais B, Cabasson C, Maucourt M, Bernillon S, Moing A, Dieuaide-Noubhani M, Mazat JP, Gibon Y. Respiration climacteric in tomato fruits elucidated by constraint-based modelling. New Phytol. 2017 Mar;213(4):1726-1739

Millet AM, Bertholet AM, Daloyau M, Reynier P, Galinier A, Devin A, Wissinguer B, Belenguer P, Davezac N. Loss of functional OPA1 unbalances redox state: implications in dominant optic atrophy pathogenesis. Ann Clin Transl Neurol. 2016 Jun;3(6):408-21

Kühl I, Miranda M, Posse V, Milenkovic D, Mourier A, Siira SJ, Bonekamp NA, Neumann U, Filipovska A, Polosa PL, Gustafsson CM, Larsson NG. POLRMT regulates the switch between replication primer formation and gene expression of mammalian mtDNA. Sci Adv. 2016 Aug;2(8):e1600963

Rackham O, Busch JD, Matic S, Siira SJ, Kuznetsova I, Atanassov I, Ermer JA, Shearwood AM, Richman TR, Stewart JB, Mourier A, Milenkovic D, Larsson NG, Filipovska A. Hierarchical RNA Processing Is Required for Mitochondrial Ribosome Assembly. Cell Rep. 2016 Aug 16;16(7):1874-90

Vajrala VS, Suraniti E, Rigoulet M, Devin A, Sojic N, Arbault S. PDMS microwells for multi-parametric monitoring of single mitochondria on a large scale: a study of their individual membrane potential and endogenous NADH. Integr Biol (Camb). 2016 Aug 8;8(8):836-43

Hammad N, Rosas-Lemus M, Uribe-Carvajal S, Rigoulet M, Devin A. The Crabtree and Warburg effects: Do metabolite-induced regulations participate in their induction? Biochim Biophys Acta. 2016 Aug;1857(8):1139-1146

Silva Ramos E, Larsson NG, Mourier A. Bioenergetic roles of mitochondrial fusion. Biochim Biophys Acta. 2016 Aug;1857(8):1277-1283

Avéret N, Jobin ML, Devin A, Rigoulet M. Proton pumping complex I increases growth yield in Candida utilis. Biochim Biophys Acta. 2015 Oct;1847(10):1320-6

Raoux M, Vacher P, Papin J, Picard A, Kostrzewa E, Devin A, Gaitan J, Limon I, Kas MJ, Magnan C, Lang J. Multilevel control of glucose homeostasis by adenylyl cyclase 8. Diabetologia. 2015 Apr;58(4):749-57

Cornish-Bowden A, Mazat JP, Nicolas S. Victor Henri: 111 years of his equation. Biochimie. 2014 Dec;107 Pt B:161-6

Beauvoit BP, Colombié S, Monier A, Andrieu MH, Biais B, Bénard C, Chéniclet C, Dieuaide-Noubhani M, Nazaret C, Mazat JP, Gibon Y. Model-assisted analysis of sugar metabolism throughout tomato fruit development reveals enzyme and carrier properties in relation to vacuole expansion. Plant Cell. 2014 Aug;26(8):3224-42

Heiske M, Nazaret C, Mazat JP. Modeling the respiratory chain complexes with biothermokinetic equations - the case of complex I. Biochim Biophys Acta. 2014 Oct;1837(10):1707-16

Yoboue ED, Mougeolle A, Kaiser L, Averet N, Rigoulet M, Devin A. The role of mitochondrial biogenesis and ROS in the control of energy supply in proliferating cells. Biochim Biophys Acta. 2014 Jul;1837(7):1093-8

Mazat JP, Ransac S, Heiske M, Devin A, Rigoulet M. Mitochondrial energetic metabolism-some general principles. IUBMB Life. 2013 Mar;65(3):171-9

Baret P, Septembre-Malaterre A, Rigoulet M, Lefebvre d'Hellencourt C, Priault M, Gonthier MP, Devin A. Dietary polyphenols preconditioning protects 3T3-L1 preadipocytes from mitochondrial alterations induced by oxidative stress. Int J Biochem Cell Biol. 2013 Jan;45(1):167-74

Yoboue ED, Devin A. Reactive oxygen species-mediated control of mitochondrial biogenesis. Int J Cell Biol. 2012;2012:403870

Casteilla L, Devin A, Salin B, Averet N, Rigoulet M. UCP1 as a water/proton co-transporter. Mitochondrion. 2012 Jul;12(4):480-1

Ransac S, Heiske M, Mazat JP. From in silico to in spectro kinetics of respiratory complex I. Biochim Biophys Acta. 2012 Oct;1817(10):1958-69

Yoboue ED, Augier E, Galinier A, Blancard C, Pinson B, Casteilla L, Rigoulet M, Devin A. cAMP-induced mitochondrial compartment biogenesis: role of glutathione redox state. J Biol Chem. 2012 Apr 27;287(18):14569-78

Gutiérrez Cortés N, Pertuiset C, Dumon E, Börlin M, Hebert-Chatelain E, Pierron D, Feldmann D, Jonard L, Marlin S, Letellier T, Rocher C. Novel mitochondrial DNA mutations responsible for maternally inherited nonsyndromic hearing loss. Hum Mutat. 2012 Apr;33(4):681-9

Casteilla L, Devin A, Carriere A, Salin B, Schaeffer J, Rigoulet M. Control of mitochondrial volume by mitochondrial metabolic water. Mitochondrion. 2011 Nov;11(6):862-6

Pérès S, Vallée F, Beurton-Aimar M, Mazat JP. ACoM: A classification method for elementary flux modes based on motif finding. Biosystems. 2011 Mar;103(3):410-9

Diaz-Ruiz R, Rigoulet M, Devin A. The Warburg and Crabtree effects: On the origin of cancer cell energy metabolism and of yeast glucose repression. Biochim Biophys Acta. 2011 Jun;1807(6):568-76

Rigoulet M, Yoboue ED, Devin A. Mitochondrial ROS generation and its regulation: mechanisms involved in H(2)O(2) signaling. Antioxid Redox Signal. 2011 Feb 1;14(3):459-68

Rigoulet M, Mourier A, Galinier A, Casteilla L, Devin A. Electron competition process in respiratory chain: regulatory mechanisms and physiological functions. Biochim Biophys Acta. 2010 Jun-Jul;1797(6-7):671-7

Chevtzoff C, Yoboue ED, Galinier A, Casteilla L, Daignan-Fornier B, Rigoulet M, Devin A. Reactive oxygen species-mediated regulation of mitochondrial biogenesis in the yeast Saccharomyces cerevisiae. J Biol Chem. 2010 Jan 15;285(3):1733-42

Diaz-Ruiz R, Uribe-Carvajal S, Devin A, Rigoulet M. Tumor cell energy metabolism and its common features with yeast metabolism. Biochim Biophys Acta. 2009 Dec;1796(2):252-65

Noubhani A, Bunoust O, Bonini BM, Thevelein JM, Devin A, Rigoulet M. The trehalose pathway regulates mitochondrial respiratory chain content through hexokinase 2 and cAMP in Saccharomyces cerevisiae. J Biol Chem. 2009 Oct 2;284(40):27229-34

 

Liste complète des publications sur Pubmed