Citric Acid Cycle and Oxidative Phosphorylation

Evolution of the enzymes of the citric acid cycle and the glyoxylate cycle of higher plants A case study of endosymbiotic gene transfer Claus Schnarrenberger 1 and William Martin 2 1 Institut fu È r Biologie, Freie Universita È t Berlin, Germany; 2 Institut fu È r Botanik III, Universita È tDu È sseldorf, Germany The citric acid or tricarboxylic acid cycle is a central element of higher-plant carbon metabolism which p rovides, among other things, electrons for oxidative phosphorylation i n t he inner mitochondrial membrane, intermediates for amin o- acid biosynthesis, and oxaloacetate for gluconeogenesis from succinate derived from fatty acids via the glyoxylate cycle in g lyoxysomes. The tricarboxylic acid cycle is a typical mitochondrial pathway and is widespread among a-pro- teobacteria, the group of eubacteria as de®ned under rRNA systematics f rom w hich mitochondria arose. Most of the enzymes of the tricarboxylic acid cycle are encoded in the nucleus in higher eukaryotes, and several have been previ- ously shown to branch with their homologues from a-pro- teobacteria, indicating that the eukaryotic nuclear genes were acquired from the mitochondrial genome during the course of evolution. Here, we investigate the individual evolutionary histories o f all of the enzymes of the tricar- boxylic acid c ycle and the glyoxylate cycle using p rotein maximum likelihood phylogenies, focusing on t he evo lu- tionary origin of the nuclear-encoded proteins in higher plants. The results indicate that about half of the proteins involved in this eukaryo tic pathway a re most similar t o their a-proteobacterial homologues, whereas the remainder are most similar to eubacterial, but not speci®cally a-proteo- bacterial, homologues. A consideration of (a) the process of lateral gene transfer among free-living prokaryotes and ( b) the mechanistics of endosymbiotic (symbiont-to-host) gene transfer reveals that it i s unrealistic t o expect a ll nuclear genes that were acquired from the a-proteobacterial ancestor of mitochondria to branch speci®cally with their homologues encoded in the genomes o f contemporary a-proteobacteria. Rather, even if molecular phylogenetics were to work perfectly ( which i t does not), then some nuclear-encoded proteins that were acquired from the a-proteobacterial ancestor of mitochondria should, in phylogenetic t rees, branch with homologues that are no longer found in most a-proteobacterial genomes, and some should reside on long branches that reveal anity to eubacterial rather than archaebacterial homologues, but no particular anity for any speci®c eubacterial donor. Keywords: glyoxysomes; microbodies; mitochondria; pathway evolution, pyruvate dehydrogenase. Metabolic pathways are units of biochemical function that encompass a number of su bstrate conversions leading from one chemical intermediate to another. The large amounts of accumulated sequence data from prokaryotic and eukary- otic sources provide novel opportunities to study the molecular evolution not only o f individual enzymes, b ut also of individual pathways consisting of several enzymatic substrate conversions. This opens the door to a number of new and intriguing questions in m olecular e volution, s uch a s the following. Were pathways assembled originally during the early phases of biochemical evolution, and subsequently been passed down through inheritance ever since? Do pathways evolve as coherent entities consisting o f the same group Citric Acid Cycle and Oxidative Phosphorylation Citric Acid Cycle and Oxidative Phosphorylation Bởi: OpenStaxCollege The Citric Acid Cycle In eukaryotic cells, the pyruvate molecules produced at the end of glycolysis are transported into mitochondria, which are sites of cellular respiration If oxygen is available, aerobic respiration will go forward In mitochondria, pyruvate will be transformed into a two-carbon acetyl group (by removing a molecule of carbon dioxide) that will be picked up by a carrier compound called coenzyme A (CoA), which is made from vitamin B5 The resulting compound is called acetyl CoA ([link]) Acetyl CoA can be used in a variety of ways by the cell, but its major function is to deliver the acetyl group derived from pyruvate to the next pathway in glucose catabolism Pyruvate is converted into acetyl-CoA before entering the citric acid cycle Like the conversion of pyruvate to acetyl CoA, the citric acid cycle in eukaryotic cells takes place in the matrix of the mitochondria Unlike glycolysis, the citric acid cycle is a closed loop: The last part of the pathway regenerates the compound used in the first step The eight steps of the cycle are a series of chemical reactions that produces two carbon dioxide molecules, one ATP molecule (or an equivalent), and reduced forms (NADH and FADH2) of NAD+ and FAD+, important coenzymes in the cell Part of this is considered an aerobic pathway (oxygen-requiring) because the NADH and FADH2 1/6 Citric Acid Cycle and Oxidative Phosphorylation produced must transfer their electrons to the next pathway in the system, which will use oxygen If oxygen is not present, this transfer does not occur Two carbon atoms come into the citric acid cycle from each acetyl group Two carbon dioxide molecules are released on each turn of the cycle; however, these not contain the same carbon atoms contributed by the acetyl group on that turn of the pathway The two acetyl-carbon atoms will eventually be released on later turns of the cycle; in this way, all six carbon atoms from the original glucose molecule will be eventually released as carbon dioxide It takes two turns of the cycle to process the equivalent of one glucose molecule Each turn of the cycle forms three high-energy NADH molecules and one high-energy FADH2 molecule These high-energy carriers will connect with the last portion of aerobic respiration to produce ATP molecules One ATP (or an equivalent) is also made in each cycle Several of the intermediate compounds in the citric acid cycle can be used in synthesizing non-essential amino acids; therefore, the cycle is both anabolic and catabolic Oxidative Phosphorylation You have just read about two pathways in glucose catabolism—glycolysis and the citric acid cycle—that generate ATP Most of the ATP generated during the aerobic catabolism of glucose, however, is not generated directly from these pathways Rather, it derives from a process that begins with passing electrons through a series of chemical reactions to a final electron acceptor, oxygen These reactions take place in specialized protein complexes located in the inner membrane of the mitochondria of eukaryotic organisms and on the inner part of the cell membrane of prokaryotic organisms The energy of the electrons is harvested and used to generate a electrochemical gradient across the inner mitochondrial membrane The potential energy of this gradient is used to generate ATP The entirety of this process is called oxidative phosphorylation The electron transport chain ([link]a) is the last component of aerobic respiration and is the only part of metabolism that uses atmospheric oxygen Oxygen continuously diffuses into plants for this purpose In animals, oxygen enters the body through the respiratory system Electron transport is a series of chemical reactions that resembles a bucket brigade in that electrons are passed rapidly from one component to the next, to the endpoint of the chain where oxygen is the final electron acceptor and water is produced There are four complexes composed of proteins, labeled I through IV in [link]c, and the aggregation of these four complexes, together with associated mobile, accessory electron carriers, is called the electron transport chain The electron transport chain is present in multiple copies in the inner mitochondrial membrane of eukaryotes and in the plasma membrane of prokaryotes In each transfer of an electron through the electron transport chain, the electron loses energy, but with some transfers, the energy is stored as potential energy by using it to pump hydrogen ions across the inner 2/6 Citric Acid Cycle and Oxidative Phosphorylation mitochondrial membrane into the intermembrane space, creating an electrochemical gradient Art Connection (a) The electron transport chain is a set of molecules that supports a series of oxidationreduction reactions (b) ATP synthase is a complex, molecular machine that uses an H+ gradient to regenerate ATP from ADP (c) Chemiosmosis ... 1 CHAPTER 4: THE CITRIC ACID AND OXIDATIVE PHOSPHORYLATION INTERNATIONAL UNIVERSITY SCHOOL OF BIOTECHNOLOGY BIOCHEMISTRY 2 Learning objectives 1. To understand the intermediates in CAC 2. The ATPs produce in CAC 3. The CO2 is released in CAC 4. The electrons are transferred in the electron transport chain 5. The oxidative phosphorylation 3 Content Citric acid cycle Introduction Cellular location Catabolism Anabolism & catabolism Sources of acetyl-CoA Fatty acid –aminoacid- monosaccharides 4 Content Reactants & products Cyclical reaction pathway Fate of acetyl CoA carbon regulation: inhibition Energetics Anaerobic Anaplerotic reactions Oxidative phoshorylation Introduction Mitochondrial anatomy Shuttle system Introduction to the transport chain Comlex I- comlex II- comlex III and Cytochrome C- comlex IV 5 Citric Acid Cycle INTRODUCTION The citric acid cycle is a central metabolic pathway that completes the oxidative degradation of fatty acids, amino acids, and monosaccharides. During aerobic catabolism, these biomolecules are broken down to smaller molecules that ultimately contribute to a cell’s energetic or molecular needs. 6 FIG. 01: Citric acid cycle is the central metabolic pathway 7 INTRODUCTION Early metabolic steps, including glycolysis and the activity of the pyruvate dehydrogenase complex, yield a two-carbon fragment called an acetyl group, which is linked to a large cofactor known as coenzyme A (or CoA). It is during the citric acid cycle that acetyl-CoA is oxidized to the waste product, carbon dioxide, along with the reduction of the cofactors NAD+ and ubiquinone. 8 FIG. 02: Early catabolic pathway 9 FIG. 03: Citric acid cycle is the central metabolic pathway 10 INTRODUCTION The citric acid cycle serves two main purposes: 1.To increase the cell’s ATP-producing potential by generating a reduced electron carriers such as NADH and reduced ubiquinone; and 2.To provide the cell with a variety of metabolic precursors. [...]... carriers and their role in coupling the citric acid cycle to downstream reactions that produce ATP; Describe the amphibolic character of the citric acid cycle; and Understand the reactions that replenish citric acid cycle intermediates 13 CELLULAR LOCATION Both prokaryotic and eukaryotic cells use the citric acid cycle to help meet their energetic and molecular needs In respiring prokaryotes, the citric acid. ..FIG 04: Main purposes of CAC 11 INTRODUCTION Be able to describe the sources of acetyl groups that enter the citric acid cycle; Trace the conversion of substrates to products through each of the citric acid cycle’s eight reactions and understand how flux through the cycle is regulated; Understand the energetic output of the citric acid cycle; 12 INTRODUCTION Describe the role of the reduced... and degrading molecules are considered amphibolic Amphi is a Greek prefix meaning both 23 FIG 10: The CAC is amphibolic 24 SOURCES OF ACETYL-CoA 25 The skeleton drawings of the monosaccharide glucose, the fatty acid palmitic acid, BioMed Central Page 1 of 11 (page number not for citation purposes) Theoretical Biology and Medical Modelling Open Access Research Kinetic modeling of tricarboxylic acid cycle and glyoxylate bypass in Mycobacterium tuberculosis, and its application to assessment of drug targets Vivek Kumar Singh and Indira Ghosh* Address: Bioinformatics Centre, University of Pune, Pune-411007, India Email: Vivek Kumar Singh - vivek@bioinfo.ernet.in; Indira Ghosh* - indira@bioinfo.ernet.in * Corresponding author Abstract Background: Targeting persistent tubercule bacilli has become an important challenge in the development of anti-tuberculous drugs. As the glyoxylate bypass is essential for persistent bacilli, interference with it holds the potential for designing new antibacterial drugs. We have developed kinetic models of the tricarboxylic acid cycle and glyoxylate bypass in Escherichia coli and Mycobacterium tuberculosis, and studied the effects of inhibition of various enzymes in the M. tuberculosis model. Results: We used E. coli to validate the pathway-modeling protocol and showed that changes in metabolic flux can be estimated from gene expression data. The M. tuberculosis model reproduced the observation that deletion of one of the two isocitrate lyase genes has little effect on bacterial growth in macrophages, but deletion of both genes leads to the elimination of the bacilli from the lungs. It also substantiated the inhibition of isocitrate lyases by 3-nitropropionate. On the basis of our simulation studies, we propose that: (i) fractional inactivation of both isocitrate dehydrogenase 1 and isocitrate dehydrogenase 2 is required for a flux through the glyoxylate bypass in persistent mycobacteria; and (ii) increasing the amount of active isocitrate dehydrogenases can stop the flux through the glyoxylate bypass, so the kinase that inactivates isocitrate dehydrogenase 1 and/or the proposed inactivator of isocitrate dehydrogenase 2 is a potential target for drugs against persistent mycobacteria. In addition, competitive inhibition of isocitrate lyases along with a reduction in the inactivation of isocitrate dehydrogenases appears to be a feasible strategy for targeting persistent mycobacteria. Conclusion: We used kinetic modeling of biochemical pathways to assess various potential anti- tuberculous drug targets that interfere with the glyoxylate bypass flux, and indicated the type of inhibition needed to eliminate the pathogen. The advantage of such an approach to the assessment of drug targets is that it facilitates the study of systemic effect(s) of the modulation of the target enzyme(s) in the cellular environment. Background Tuberculosis is an ancient disease that has plagued humans for centuries, and presently there is an urgent need for new drugs to combat drug-resistant tuberculosis Published: 03 August 2006 Theoretical Biology and Medical Modelling 2006, 3:27 doi:10.1186/1742-4682-3-27 Received: 03 April 2006 Accepted: 03 August 2006 This article is available from: http://www.tbiomed.com/content/3/1/27 © 2006 Singh and Ghosh; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0 ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Theoretical Biology and Medical Modelling 2006, 3:27 http://www.tbiomed.com/content/3/1/27 Page 2 of 11 (page number not for citation purposes) and shorten the time of tuberculosis therapy. Tuberculosis treatment is lengthy because of a population of persistent bacilli that is not effectively eliminated by current drugs. The persistent bacilli primarily use fatty acids as their car- bon source [1]. This makes the glyoxylate bypass, consist- ing of isocitrate lyase (ICL) and malate synthase (MS), essential for the bacterium; in its absence there will be no net formation of the intermediates required for Lecture Connections 16 | The Citric Acid Cycle © 2009 W H Freeman and Company CHAPTER 16 The Citric Acid Cycle Key topics: – Cellular respiration – Conversion of pyruvate to activated acetate – Reactions of the citric acid cycle – Regulation of the citric acid cycle – Conversion of acetate to carbohydrate precursors in the glyoxylate cycle Only a Small Amount of Energy Available in Glucose is Captured in Glycolysis Glycolysis G’° = -146 kJ/mol GLUCOSE Full oxidation (+ O2) G’° = -2,840 kJ/mol CO2 + H2O Cellular Respiration • process in which cells consume O2 and produce CO2 • provides more energy (ATP) from glucose than glycolysis • also captures energy stored in lipids and amino acids • evolutionary origin: developed about 2.5 billion years ago • used by animals, plants, and many microorganisms • occurs in three major stages: - acetyl CoA production - acetyl CoA oxidation - electron transfer and oxidative phosphorylation Respiration: Stage Generates some: ATP, NADH, FADH2 Respiration: Stage Generates more NADH, FADH2 and one GTP Respiration: Stage Makes lots of ATP Products from One Turn of the Cycle Net Effect of the Citric Acid Cycle Acetyl-CoA + 3NAD+ + FAD + GDP + Pi + H2O 2CO2 +3NADH + FADH2 + GTP + CoA + 3H+ • carbons of acetyl groups in acetyl-CoA are oxidized to CO2 • electrons from this process reduce NAD+ and FAD • one GTP is formed per cycle, this can be converted to ATP • intermediates in the cycle are not depleted Direct and Indirect ATP Yield Role of the Citric Acid Cycle in Anabolism Anaplerotic Reactions • these reactions replenish metabolites for the cycle • four carbon intermediates are formed by carboxylation of three-carbon precursors Regulation of the Citric Acid Cycle Glyoxylate Cycle Chapter 16: Summary In this chapter, we learned that: • Citric acid cycle is an important catabolic process: it makes GTP, and reduced cofactors that could yield ATP • Citric acid cycle plays important anabolic roles in the cell • A large multi-subunit enzyme, pyruvate dehydrogenase complex, converts pyruvate into acetyl-CoA • Several cofactors are involved in reactions that harness the energy from pyruvate • The rules of organic chemistry help to rationalize reactions in the citric acid cycle ... each cycle Several of the intermediate compounds in the citric acid cycle can be used in synthesizing non-essential amino acids; therefore, the cycle is both anabolic and catabolic Oxidative Phosphorylation. .. as the electron transporter in the liver and FAD+ in the brain, so ATP yield depends on the tissue being considered 4/6 Citric Acid Cycle and Oxidative Phosphorylation Another factor that affects... and lipids These same molecules, except nucleic acids, can serve as energy sources for the glucose pathway 5/6 Citric Acid Cycle and Oxidative Phosphorylation Art Connections [link] Cyanide inhibits