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The Switch from Fermentation to Respiration in Saccharomyces Cerevisiae Is Regulated by the Ert1 Transcriptional Activator/Repressor
INVESTIGATION The Switch from Fermentation to Respiration in Saccharomyces cerevisiae Is Regulated by the Ert1 Transcriptional Activator/Repressor Najla Gasmi,* Pierre-Etienne Jacques,† Natalia Klimova,† Xiao Guo,§ Alessandra Ricciardi,§ François Robert,†,** and Bernard Turcotte*,‡,§,1 ‡Department of Medicine, *Department of Biochemistry, and §Department of Microbiology and Immunology, McGill University Health Centre, McGill University, Montreal, QC, Canada H3A 1A1, †Institut de recherches cliniques de Montréal, Montréal, QC, Canada H2W 1R7, and **Département de Médecine, Faculté de Médecine, Université de Montréal, QC, Canada H3C 3J7 ABSTRACT In the yeast Saccharomyces cerevisiae, fermentation is the major pathway for energy production, even under aerobic conditions. However, when glucose becomes scarce, ethanol produced during fermentation is used as a carbon source, requiring a shift to respiration. This adaptation results in massive reprogramming of gene expression. Increased expression of genes for gluconeogenesis and the glyoxylate cycle is observed upon a shift to ethanol and, conversely, expression of some fermentation genes is reduced. The zinc cluster proteins Cat8, Sip4, and Rds2, as well as Adr1, have been shown to mediate this reprogramming of gene expression. In this study, we have characterized the gene YBR239C encoding a putative zinc cluster protein and it was named ERT1 (ethanol regulated transcription factor 1). ChIP-chip analysis showed that Ert1 binds to a limited number of targets in the presence of glucose. The strongest enrichment was observed at the promoter of PCK1 encoding an important gluconeogenic enzyme. With ethanol as the carbon source, enrichment was observed with many additional genes involved in gluconeogenesis and mitochondrial function. Use of lacZ reporters and quantitative RT-PCR analyses demonstrated that Ert1 regulates expression of its target genes in a manner that is highly redundant with other regulators of gluconeogenesis. -
Amphibolic Nature of Krebs Cycle
Amphibolic nature of Krebs Cycle How what we are is what we eat • In aerobic organisms, the citric acid cycle is an amphibolic pathway, one that serves in both catabolic and anabolic processes. • Since the citric acid does both synthesis (anabolic) and breakdown (catabolic) activities, it is called an amphibolic pathway • The citric acid cycle is amphibolic (i.e it is both anabolic and catabolic in its function). • It is said to be an AMPHIBOLIC pathway, because it functions in both degradative or catabolic and biosynthetic or anabolic reactions (amphi = both) A central metabolic pathway or amphibolic pathway is a set of reactions which permit the interconversion of several metabolites, and represents the end of the catabolism and the beginning of anabolism • The KREBS CYCLE or citric acid cycle is a series of reactions that degrades acetyl CoA to yield carbon dioxide, and energy, which is used to produce NADH, H+ and FADH. • The KREBS CYCLE connects the catabolic pathways that begin with the digestion and degradation of foods in stages 1 and 2 with the oxidation of substrates in stage 3 that generates most of the energy for ATP synthesis. • The citric acid cycle is the final common pathway in the oxidation of fuel molecules. In stage 3 of metabolism, citric acid is a final common catabolic intermediate in the form of acetylCoA. • This is why the citric acid cycle is called a central metabolic pathway. Anaplerosis and Cataplerosis Anaplerosis is a series of enzymatic reactions in which metabolic intermediates enter the citric acid cycle from the cytosol. Cataplerosis is the opposite, a process where intermediates leave the citric acid cycle and enter the cytosol. -
The Syntrophy Hypothesis for the Origin of Eukaryotes Revisited Purificación López-García, David Moreira
The Syntrophy hypothesis for the origin of eukaryotes revisited Purificación López-García, David Moreira To cite this version: Purificación López-García, David Moreira. The Syntrophy hypothesis for the origin of eukaryotes revisited. Nature Microbiology, Nature Publishing Group, 2020, 5 (5), pp.655-667. 10.1038/s41564- 020-0710-4. hal-02988531 HAL Id: hal-02988531 https://hal.archives-ouvertes.fr/hal-02988531 Submitted on 3 Dec 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. 1 2 Perspectives 3 4 5 6 The Syntrophy hypothesis for the origin of eukaryotes revisited 7 8 Purificación López-García1 and David Moreira1 9 10 1 Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France 11 12 13 14 *Correspondence to: [email protected] 15 16 17 18 19 1 20 The discovery of Asgard archaea, phylogenetically closer to eukaryotes than other archaea, together with 21 improved knowledge of microbial ecology impose new constraints on emerging models for the origin of the 22 eukaryotic cell (eukaryogenesis). Long-held views are metamorphosing in favor of symbiogenetic models 23 based on metabolic interactions between archaea and bacteria. These include the classical Searcy’s and 24 hydrogen hypothesis, and the more recent Reverse Flow and Entangle-Engulf-Enslave (E3) models. -
Effects of Glucagon, Glycerol, and Glucagon Plus Glycerol On
Iowa State University Capstones, Theses and Graduate Theses and Dissertations Dissertations 2011 Effects of glucagon, glycerol, and glucagon plus glycerol on gluconeogenesis, lipogenesis, and lipolysis in periparturient Holstein cows Nimer Mehyar Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/etd Part of the Biochemistry, Biophysics, and Structural Biology Commons Recommended Citation Mehyar, Nimer, "Effects of glucagon, glycerol, and glucagon plus glycerol on gluconeogenesis, lipogenesis, and lipolysis in periparturient Holstein cows" (2011). Graduate Theses and Dissertations. 11923. https://lib.dr.iastate.edu/etd/11923 This Thesis is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Effects of glucagon, glycerol, and glucagon plus glycerol on gluconeogenesis, lipogenesis, and lipolysis in periparturient Holstein cows by Nimer Mehyar A thesis submitted to graduate faculty in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE Major: Biochemistry Program of Study Committee: Donald C. Beitz, Major Professor Ted W. Huiatt Kenneth J. Koehler Iowa State University Ames, Iowa 2011 Copyright Nimer Mehyar, 2011. All rights reserved ii To My Mother To Ghada Ali, Sarah, and Hassan -
Exam #2 Review
Exam #2 Review Exam #2 will cover all the material that has been presented in class since Exam #1 and up through the metabolism introduction. This includes eukaryotic cell structure / function, transport, the closed system growth curve, enzymes and the introduction to metabolism. As always, it is best to begin by studying your notes and then after you feel your study is complete, take some time to look through this review. I. Eukaryotic cell structure / function A. There is a great deal of variance among eukaryotic cells - from protozoan cells to yeast cells to human cells. Fungi and protists (classically split into algae and protozoa) are eukaryotic representatives of the microbial world. B. Structure of the eukaryotic cell. 1. Cytoskeleton - provides structure and shape of cell, three components: a. Microtubules - largest element of cytoskeleton, composed of hollow cylinders of tubulin, form mitotic spindles, cilia and flagella and cell “highways”. b. Microfilaments - smallest element of cytoskeleton, composed of actin, involved in motion (pseudopod formation). c. Intermediate filaments - very stable structural element, play a supportive role, composed of proteins including keratin. Practice: Microfilaments a. are a component of the cytoskeleton. b. are long, twisted polymers of a protein called actin. c. form eukaryotic flagella. d. are made of tubulin. e. a and b f. c and d 2. Nucleus a. Bound by both an inner and outer membrane. The space between the two membranes is called the perinuclear space. The membrane has large nuclear pores through which proteins can pass (Why is this important?) b. Linear pieces of DNA are packaged by wrapping one and three quarters times around a histone octamer to form a core particle. -
• Glycolysis • Gluconeogenesis • Glycogen Synthesis
Carbohydrate Metabolism! Wichit Suthammarak – Department of Biochemistry, Faculty of Medicine Siriraj Hospital – Aug 1st and 4th, 2014! • Glycolysis • Gluconeogenesis • Glycogen synthesis • Glycogenolysis • Pentose phosphate pathway • Metabolism of other hexoses Carbohydrate Digestion! Digestive enzymes! Polysaccharides/complex carbohydrates Salivary glands Amylase Pancreas Oligosaccharides/dextrins Dextrinase Membrane-bound Microvilli Brush border Maltose Sucrose Lactose Maltase Sucrase Lactase ‘Disaccharidase’ 2 glucose 1 glucose 1 glucose 1 fructose 1 galactose Lactose Intolerance! Cause & Pathophysiology! Normal lactose digestion Lactose intolerance Lactose Lactose Lactose Glucose Small Intestine Lactase lactase X Galactose Bacteria 1 glucose Large Fermentation 1 galactose Intestine gases, organic acid, Normal stools osmotically Lactase deficiency! active molecules • Primary lactase deficiency: อาการ! genetic defect, การสราง lactase ลด ลงเมออายมากขน, พบมากทสด! ปวดทอง, ถายเหลว, คลนไสอาเจยนภาย • Secondary lactase deficiency: หลงจากรบประทานอาหารทม lactose acquired/transient เชน small bowel เปนปรมาณมาก เชนนม! injury, gastroenteritis, inflammatory bowel disease! Absorption of Hexoses! Site: duodenum! Intestinal lumen Enterocytes Membrane Transporter! Blood SGLT1: sodium-glucose transporter Na+" Na+" •! Presents at the apical membrane ! of enterocytes! SGLT1 Glucose" Glucose" •! Co-transports Na+ and glucose/! Galactose" Galactose" galactose! GLUT2 Fructose" Fructose" GLUT5 GLUT5 •! Transports fructose from the ! intestinal lumen into enterocytes! -
Novel Industrial Bioprocesses for Production of Key Valuable Steroid Precursors from Phytosterol
Novel industrial bioprocesses for production of key valuable steroid precursors from phytosterol Project acronym: MySterI (Mycobacterial Steroids for Industry) Project no: EIB.12.010 Name: Carlos Barreiro ERA‐IB‐2 final conference, Berlin, 16./17.02.2016 Project partners 2 Research Centres 2 Universities 1 SME 1 Large Enterprise Project acronym: MySterI ERA‐IB‐2 Final conference, Berlin, 16./17.02.2016 www.era‐ib.net P1: INBIOTEC Project partners • P1: COORDINATOR: Asociación de investigación‐ INBIOTEC‐Instituto de Biotecnología de León (Research Centre). León (Spain). • Dr. Carlos Barreiro, Dr. Antonio Rodríguez‐García, Dr. Alberto Sola‐Landa MySterI tasks of INBOTEC: ‐Genome sequencing Mycobacterium sp NRRL B‐3805 ‐Genome mining and annotation ‐Transcriptomics (microarrays, RNAseq) ‐Proteomics (secretome analysis) • Total project budget: 93 000 € Project acronym: MySterI ERA‐IB‐2 Final conference, Berlin, 16./17.02.2016 www.era‐ib.net P2: Pharmins ltd. Project partners • P2: Pharmins Ltd. (SME) Pushchino (Russian Federation) • Dr. Marina Donova MySterI tasks of Pharmins: ‐Genome sequencing Mycobacterium sp NRRL B‐3805 ‐Biochemical characterization of proteins ‐Sterol conversion by modified mycobacterial strains ‐Two‐steps fermentation to obtain 11‐α‐OH‐AD ‐Modification of 11α‐hydroxylase enzymes • Total project budget: 123 743 € Project acronym: MySterI ERA‐IB‐2 Final conference, Berlin, 16./17.02.2016 www.era‐ib.net P3: University of York Project partners • P3: University of York (University) York (UK) • Professor Maggie Smith, Dr Jessica Loraine MySterI tasks of U. of York: ‐Genome sequencing Mycobacterium sp NRRL B‐3805 ‐Genetic tools and strain development ‐Development of DNA transformation procedures ‐Development of gene knock‐out techniques ‐Development of promoters to control gene expression • Total project budget: 312 246€ Project acronym: MySterI ERA‐IB‐2 Final conference, Berlin, 16./17.02.2016 www.era‐ib.net P4: Stiftelsen SINTEF Project partners • P4: Stiftelsen SINTEF (Research centre). -
STEREOSELECTIVE GLYCOSYLATIONS and SYNTHESIS of HYALURONAN BIOSYNTHESIS INHIBITORS by Gilbert Ochieng Wasonga a THESIS Submitted
STEREOSELECTIVE GLYCOSYLATIONS AND SYNTHESIS OF HYALURONAN BIOSYNTHESIS INHIBITORS By Gilbert Ochieng Wasonga A THESIS Submitted to Michigan State University in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE CHEMISTRY 2010 1 ABSTRACT STEREOSELECTIVE GLYCOSYLATIONS AND SYNTHESIS OF HYALURONAN SYNTHESIS INHIBITORS By Gilbert Ochieng Wasonga Stereochemical control is an important issue in carbohydrate synthesis. Glycosyl donors with participating acyl protective groups on 2-O have been shown to give 1,2-trans glycosides reliably under the pre-activation based reaction condition. In this work, the effects of additives and reaction solvent on stereoselectivity was examined using donors without participating protective groups on 2-O. We have established that the stereoselectivity could be directed by reaction solvent. The trend of stereochemical dependence on reaction solvent was applicable to a variety of reactions including the selective formation of β-mannosides. In the second part, 3-MeO-GlcNAc is efficiently prepared using a furanose oxazoline intermediate which is well suited for large scale synthesis without the need for extensive column chromatography. In addition, we have developed a robust and rapid procedure for the synthesis of 3-F-GlcNAc derivative required for inhibition studies of hyaluronan biosynthesis. In the course of our synthesis, we have shown the expanded utility of Lattrell-Dax method for carbohydrate epimerization reactions. II ACKNOWLEDGMENTS I would like to thank my advisor Professor Xuefei Huang for his guidance and support that have been instrumental in my graduate studies. Along the way, I have had the opportunity to be mentored by Doctor Youlin Zeng who was a very helpful mentor at the beginning of my chemistry research experience and I will always be grateful to him. -
Secretin and Autism: a Clue but Not a Cure
SCIENCE & MEDICINE Secretin and Autism: A Clue But Not a Cure by Clarence E. Schutt, Ph.D. he world of autism has been shaken by NBC’s broadcast connections could not be found. on Dateline of a film segment documenting the effect of Tsecretin on restoring speech and sociability to autistic chil- The answer was provided nearly one hundred years ago by dren. At first blush, it seems unlikely that an intestinal hormone Bayless and Starling, who discovered that it is not nerve signals, regulating bicarbonate levels in the stomach in response to a but rather a novel substance that stimulates secretion from the good meal might influence the language centers of the brain so cells forming the intestinal mucosa. They called this substance profoundly. However, recent discoveries in neurobiology sug- “secretin.” They suggested that there could be many such cir- gest several ways of thinking about the secretin-autism connec- culating substances, or molecules, and they named them “hor- tion that could lead to the breakthroughs we dream about. mones” based on the Greek verb meaning “to excite”. As a parent with more than a decade of experience in consider- A simple analogy might help. If the body is regarded as a commu- ing a steady stream of claims of successful treatments, and as a nity of mutual service providers—the heart and muscles are the pri- scientist who believes that autism is a neurobiological disorder, I mary engines of movement, the stomach breaks down foods for have learned to temper my hopes about specific treatments by distribution, the liver detoxifies, and so on—then the need for a sys- seeing if I could construct plausible neurobiological mechanisms tem of messages conveyed by the blood becomes clear. -
Fatty Acid Biosynthesis
BI/CH 422/622 ANABOLISM OUTLINE: Photosynthesis Carbon Assimilation – Calvin Cycle Carbohydrate Biosynthesis in Animals Gluconeogenesis Glycogen Synthesis Pentose-Phosphate Pathway Regulation of Carbohydrate Metabolism Anaplerotic reactions Biosynthesis of Fatty Acids and Lipids Fatty Acids contrasts Diversification of fatty acids location & transport Eicosanoids Synthesis Prostaglandins and Thromboxane acetyl-CoA carboxylase Triacylglycerides fatty acid synthase ACP priming Membrane lipids 4 steps Glycerophospholipids Control of fatty acid metabolism Sphingolipids Isoprene lipids: Cholesterol ANABOLISM II: Biosynthesis of Fatty Acids & Lipids 1 ANABOLISM II: Biosynthesis of Fatty Acids & Lipids 1. Biosynthesis of fatty acids 2. Regulation of fatty acid degradation and synthesis 3. Assembly of fatty acids into triacylglycerol and phospholipids 4. Metabolism of isoprenes a. Ketone bodies and Isoprene biosynthesis b. Isoprene polymerization i. Cholesterol ii. Steroids & other molecules iii. Regulation iv. Role of cholesterol in human disease ANABOLISM II: Biosynthesis of Fatty Acids & Lipids Lipid Fat Biosynthesis Catabolism Fatty Acid Fatty Acid Degradation Synthesis Ketone body Isoprene Utilization Biosynthesis 2 Catabolism Fatty Acid Biosynthesis Anabolism • Contrast with Sugars – Lipids have have hydro-carbons not carbo-hydrates – more reduced=more energy – Long-term storage vs short-term storage – Lipids are essential for structure in ALL organisms: membrane phospholipids • Catabolism of fatty acids –produces acetyl-CoA –produces reducing -
Cori Cycle Activity in Man
Cori cycle activity in man Christine Waterhouse, Julian Keilson J Clin Invest. 1969;48(12):2359-2366. https://doi.org/10.1172/JCI106202. Research Article 12 subjects have been studied after an overnight fast with trace amounts of pyruvate-3-14C and glucose-6-14C. Blood disappearance curves and incorporation of the pyruvate-3-14C label into blood glucose have been determined. By the use of transfer functions which allow processes with many different chemical steps to be examined as a unit, we have determined the per cent of pyruvate and presumably lactate which is regenerated into glucose. 8 of the 12 subjects showed that 7-23 mg/kg per hr are recycled, while 4 subjects fell well outside this range. Correlation of increased activity was not good with any demonstrated metabolic abnormality (diabetes or obesity), and it is suggested from clinical observation of the subjects that anxiety may play a role. Find the latest version: https://jci.me/106202/pdf Cori Cycle Activity in Man CHRISTIE WATERHOUSE and JULLAN KEISON From the Department of Medicine, University of Rochester School of Medicine and Dentistry and the Department of Statistics, University of Rochester College of Arts and Sciences, Rochester, New York 14620 ABSTRACT 12 subjects have been studied after an glucose derived from lactate and pyruvate. The analysis overnight fast with trace amounts of pyruvate-3-'4C and itself also views glucose as distributed in a homogeneous glucose-6-'4C. Blood disappearance curves and incorpora- pool within the body, thus neglecting the early portion tion of the pyruvate-3-14C label into blood glucose have of the glucose 'C disappearance curve. -
MITOCW | 20. Bioenergetics/Intro Pathways/Glycolysis I
MITOCW | 20. Bioenergetics/Intro Pathways/Glycolysis I [SQUEAKING] [RUSTLING] [CLICKING] PROFESSOR: Today we're going to discuss bioenergetics, continue that discussion and use that as a transition into also beginning to see how that applies to understanding glycolysis, the pathway that allows glucose breakdown. So just as a reminder of a couple of the points that we discussed last time, so last time we discussed what makes reactions favorable. And so remember, you could have any reaction, A to B-- A to B could be a single step. A to B could be an entire pathway, all steps in the pathway, that whether or not that reaction or pathway happens is determined by thermodynamics. It's not determined by enzymes. Enzymes are important, of course, to control the rate of reactions so they may allow things to happen that otherwise wouldn't happen. But whether the reaction happens or not is determined by free energy. And so free energy, delta G, remember we discussed is the following relationship. So it's related to this constant delta G0 prime, which is related to the equilibrium constant for any pair of products and reactants as well as this formula rt times the log of the products over the reactants. And so remember this means that whether a reaction happens depends on the equilibrium constant, but it also depends on the actual conditions present. That is how much substrate and how much product is there. And so what this means is that biology can come up with ways by keeping the product concentrations low to do things that may move in the opposite direction of what you would predict from equilibrium.