THÈSE De DOCTORAT Mimicking C-C Bond Forming Reactions of Core
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A Dicarboxylate/4-Hydroxybutyrate Autotrophic Carbon Assimilation Cycle in the Hyperthermophilic Archaeum Ignicoccus Hospitalis
A dicarboxylate/4-hydroxybutyrate autotrophic carbon assimilation cycle in the hyperthermophilic Archaeum Ignicoccus hospitalis Harald Huber*†, Martin Gallenberger*, Ulrike Jahn*, Eva Eylert‡, Ivan A. Berg§, Daniel Kockelkorn§, Wolfgang Eisenreich‡, and Georg Fuchs§ *Lehrstuhl fu¨r Mikrobiologie und Archaeenzentrum, Universita¨t Regensburg, Universitaetsstrasse 31, D-93053 Regensburg, Germany; ‡Lehrstuhl fu¨r Biochemie, Department Chemie, Technische Universita¨t Mu¨ nchen, Lichtenbergstrasse 4, D-85748 Garching, Germany; and §Lehrstuhl fu¨r Mikrobiologie, Universita¨t Freiburg, Scha¨nzlestrasse 1, D-79104 Freiburg, Germany Edited by Dieter So¨ll, Yale University, New Haven, CT, and approved April 1, 2008 (received for review February 1, 2008) Ignicoccus hospitalis is an anaerobic, autotrophic, hyperthermophilic starting from acetyl-CoA (4). On the basis of these data, pyruvate Archaeum that serves as a host for the symbiotic/parasitic Archaeum synthase and phosphoenolpyruvate (PEP) carboxylase were pos- Nanoarchaeum equitans. It uses a yet unsolved autotrophic CO2 tulated as CO2 fixing enzymes, with PEP carboxylase serving as the fixation pathway that starts from acetyl-CoA (CoA), which is reduc- only enzyme used for oxaloacetate synthesis. In addition, the tively carboxylated to pyruvate. Pyruvate is converted to phosphoe- operation of an incomplete ‘‘horseshoe-type’’ citric acid cycle, in nol-pyruvate (PEP), from which glucogenesis as well as oxaloacetate which 2-oxoglutarate oxidation does not take place, was demon- formation branch off. Here, we present the complete metabolic cycle strated. Enzyme and labeling data indicated a conventional glu- by which the primary CO2 acceptor molecule acetyl-CoA is regener- coneogenesis, but with some enzymes unrelated to those of the ated. Oxaloacetate is reduced to succinyl-CoA by an incomplete classical pathway. -
Recreating Ancient Metabolic Pathways Before Enzymes Kamila B
Recreating ancient metabolic pathways before enzymes Kamila B. Muchowska, Elodie Chevallot-Beroux, Joseph Moran To cite this version: Kamila B. Muchowska, Elodie Chevallot-Beroux, Joseph Moran. Recreating ancient metabolic path- ways before enzymes. Bioorganic and Medicinal Chemistry, Elsevier, 2019, 27 (12), pp.2292-2297. 10.1016/j.bmc.2019.03.012. hal-02516541 HAL Id: hal-02516541 https://hal.archives-ouvertes.fr/hal-02516541 Submitted on 23 Mar 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. Graphical Abstract To create your abstract, type over the instructions in the template box below. Fonts or abstract dimensions should not be changed or altered. Recreating ancient metabolic pathways Leave this area blank for abstract info. before enzymes Kamila B. Muchowskaa* , Elodie Chevallot-Berouxa, and Joseph Morana* University of Strasbourg, CNRS, ISIS UMR 7006, 67000 Strasbourg, France Bioorganic & Medicinal Chemistry journal homepage: www.elsevier.com Recreating ancient metabolic pathways before enzymes Kamila B. Muchowska,a* Elodie Chevallot-Beroux,a and Joseph Morana* a University of Strasbourg, CNRS, ISIS UMR 7006, 67000 Strasbourg, France. ARTICLE INFO ABSTRACT Article history: The biochemistry of all living organisms uses complex, enzyme-catalyzed metabolic reaction Received networks. -
A Survey of Carbon Fixation Pathways Through a Quantitative Lens
Journal of Experimental Botany, Vol. 63, No. 6, pp. 2325–2342, 2012 doi:10.1093/jxb/err417 Advance Access publication 26 December, 2011 REVIEW PAPER A survey of carbon fixation pathways through a quantitative lens Arren Bar-Even, Elad Noor and Ron Milo* Department of Plant Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel * To whom correspondence should be addressed. E-mail: [email protected] Received 15 August 2011; Revised 4 November 2011; Accepted 8 November 2011 Downloaded from Abstract While the reductive pentose phosphate cycle is responsible for the fixation of most of the carbon in the biosphere, it http://jxb.oxfordjournals.org/ has several natural substitutes. In fact, due to the characterization of three new carbon fixation pathways in the last decade, the diversity of known metabolic solutions for autotrophic growth has doubled. In this review, the different pathways are analysed and compared according to various criteria, trying to connect each of the different metabolic alternatives to suitable environments or metabolic goals. The different roles of carbon fixation are discussed; in addition to sustaining autotrophic growth it can also be used for energy conservation and as an electron sink for the recycling of reduced electron carriers. Our main focus in this review is on thermodynamic and kinetic aspects, including thermodynamically challenging reactions, the ATP requirement of each pathway, energetic constraints on carbon fixation, and factors that are expected to limit the rate of the pathways. Finally, possible metabolic structures at Weizmann Institute of Science on July 3, 2016 of yet unknown carbon fixation pathways are suggested and discussed. -
SFU Thesis Template Files
Towards a Prebiotically Plausible Mechanism for the Emergence of RNA, Ribozymes and the RNA World by Lyssa Lynn Martin B.Sc., Thompson Rivers University, 2011 Thesis Submitted in Partial Fulfillment of the Requirements for the Degree of Master of Science in the Department of Molecular Biology and Biochemistry Faculty of Science Lyssa Lynn Martin 2015 SIMON FRASER UNIVERSITY Summer 2015 Approval Name: Lyssa Lynn Martin Degree: Master of Science Title: Towards a Prebiotically Plausible Mechanism for the Emergence of RNA, Ribozymes and the RNA World Examining Committee: Chair: Dr. Fredric Pio Associate Professor Peter Unrau Senior Supervisor Professor Dipankar Sen Supervisor Professor Niles Lehman Supervisor Professor Portland State University Department of Chemistry Nancy Forde Internal Examiner Associate Professor Department of Physics Date Defended/Approved: August 25, 2015 ii Abstract Available evidence, both in vitro and in vivo, attests to the descent of life from the RNA World; however, the prebiotic genesis of such RNA life remains ambiguous. How did The RNA World emerge from the abiotic chemistry on the Archean Earth? Montmorillonite clays have been shown to catalyze the polymerization of activated nucleotides (eg. adenosine 5′ phosphorimidazolide) into RNA, but polymerization has not previously been demonstrated for a prebiotically plausible nucleotide such as cyclic 2′, 3′-adenosine monophosphate (A>p). I reacted A>p in the presence of montmorillonite clay and could detect RNA polymers up to 5 nucleotides in length using a combination of HPLC, enzymatic labeling and mass spectrometry. This chemistry was found to be sensitive to pH and temperature. Reactions at pH 6 were found to produce more polymerization products than reactions at pH 7 or 8. -
The Origin of Life in the Solar System: Current Issues
Annual Reviews www.annualreviews.org/aronline Annu.Rev. EarthPlanet. Sci. 1995.23:215-49 Copyright~) 1995by AnnualReviews Inc. All rights reserved THE ORIGINOF LIFE IN THE SOLAR SYSTEM:Current Issues Christopher E Chyba White HouseFellow, National Security Council~Old Executive Office Building, Washington DC20506 Gene D. McDonald 2 Scripps Institution of Oceanography,University of California, San Diego, La Jolla, California 92093 I can see no other escapefrom this dilemma(lest our true aim be lost for ever) than that some of us shouldventure to embarkon a synthesis of facts and theories, albeit with second-hand and incompleteknowledge of someof them--and at the risk of makingfools of ourselves. Erwin Schr0dinger, What is Life? INTRODUCTION Progress in the study of the origins of life was dramatic during the decade of the 1980s. Primordial Earth was put morecompletely into the context of early Solar Systemhistory, and as this planetary view provided newinsights, other by Stanford University Libraries on 04/23/05. For personal use only. Solar Systemenvironments took on greater interest as points of comparison. Workon the energy sources needed to synthesize organic monomersor more sophisticated products on prebiotic Earth expandedwidely, with a numberof provocativenew ideas vying for attention. But mostimportantly, the elucidation Annu. Rev. Earth. Planet. Sci. 1995.23:215-249. Downloaded from arjournals.annualreviews.org of a putative RNAworld held out the hope for resolution of long-standing difficulties in the origin of DNA-proteinorganisms. This reviewis intended to report on someof the current issues in origins-of- life and exobiology research. Wetherefore cannot hope to present a compre- hensive history of the subject. -
Mitochondrial Uncoupling and the Reprograming of Intermediary Metabolism in Leukemia Cells
REVIEW ARTICLE published: 02 April 2013 doi: 10.3389/fonc.2013.00067 Mitochondrial uncoupling and the reprograming of intermediary metabolism in leukemia cells Juliana Vélez 1, Numsen Hail Jr.2,3, Marina Konopleva2,3, Zhihong Zeng 2,3, Kensuke Kojima2,3, Ismael Samudio1* and Michael Andreeff 2,3* 1 Grupo de Terapia Celular y Molecular Laboratorio de Bioquimica, Pontificia Universidad Javeriana, Bogotá, Colombia 2 Section of Molecular Hematology and Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA 3 Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA Edited by: Nearly 60 years ago Otto Warburg proposed, in a seminal publication, that an irreparable Jozsef Dudas, Medical University defect in the oxidative capacity of normal cells supported the switch to glycolysis for energy Innsbru, Austria generation and the appearance of the malignant phenotype (Warburg, 1956). Curiously, Reviewed by: Daniel Christian Hoessli, International this phenotype was also observed by Warburg in embryonic tissues, and recent research Center for Chemical and Biological demonstrated that normal stem cells may indeed rely on aerobic glycolysis – fermenting Sciences, Switzerland pyruvate to lactate in the presence of ample oxygen – rather than on the complete oxidation Jozsef Dudas, Medical University of pyruvate in the Krebs cycle – to generate cellular energy (Folmes et al., 2012). However, Innsbruck, Austria it remains to be determined whether this phenotype is causative for neoplastic develop- *Correspondence: Ismael Samudio, Laboratorio de ment, or rather the result of malignant transformation. In addition, in light of mounting Bioquimica #301, Edificio Jesús evidence demonstrating that cancer cells can carry out electron transport and oxidative Emilio Ramírez, Pontificia Universidad phosphorylation, although in some cases predominantly using electrons from non-glucose Javeriana, Cra 7 No. -
Profile of Bob B. Buchanan PROFILE
PROFILE Profile of Bob B. Buchanan PROFILE Paul Gabrielsen, Science Writer On a clear June day in 1975, Bob Buchanan and two anaerobic fermentation pro- Oslo colleagues pulled up water samples from a lake cesses responsible for their in Norway, examining the microorganisms growing at beverages. Another friend at various depths. “When we got to 6 meters,” Buchanan Duke was Melinda Speas, a recalls, “there was a band of Chlorobium growing,” graduate student in zoology. referring to a genus of green bacteria (now called Their friendship was later Chlorobaculum) that belongs to a unique class of or- rekindled in California and they ganisms called photolithotrophs. These bacteria re- married in 1965. quire sunlight for photosynthesis but obtain cellular After earning his doctorate reductants from sulfur compounds rather than water. in 1962, Buchanan secured a The bacteria buck the traditional chemical pathways postdoctoral fellowship at the for energy production and carbon fixation and instead University of California, Berkeley, use pathways discovered by Buchanan, a member of where he would spend the next the National Academy of Sciences and emeritus pro- 55 years. He hoped to work fessor at the University of California, Berkeley. with renowned microbiologist H. A. Barker, but because From Appalachia to the Laboratory Barker was on sabbatical leave Buchanan was born in 1937 in Richmond, Virginia. at the time, Buchanan instead Fearing for the family’s safety during World War II, joined the group of Barker’s Buchanan’s mother took him and his two older sisters former student, Jesse Rabinowitz. to a family farm in Southwest Virginia, near the Ap- Buchanan and Rabinowitz crys- Bob B. -
Jump-Starting a Cellular World: Investigating the Origin of Life, from Soup to Networks Richard Robinson
Open access, freely available online Feature Jump-Starting a Cellular World: Investigating the Origin of Life, from Soup to Networks Richard Robinson physicist, a chemist, and a mathematician are stranded on a desert isle, when a can of food washes up on the A beach. The three starving scientists suggest, in turn, how to open the can and ease their hunger. The physicist suggests they hurl it upon the rocks to split it open, but this fails. The chemist proposes they soak it in the sea and let the salt water eat away at the metal; again, no luck. They turn in desperation to the mathematician, who begins, “Assume we have a can opener….” When discussing the evolution of life, biologists can often sound a bit like that mathematician. Beginning with a single cell, Darwinian evolution provides a simple, robust, and powerful algorithm for deriving all the astonishing richness of life, from bacteria to brains. Natural selection and other evolutionary forces, acting on surplus populations of replicating cells and multicellular organisms, lead inevitably DOI: 10.1371/journal.pbio.0030396.g001 to evolution and adaptation. Give biologists a cell, and they’ll Figure 1. Tynagh Chimneys give you the world. But beyond assuming the fi rst cell must A view from above a chimney fi eld, showing the chimneys (round black have somehow come into existence, how do biologists explain circles) and bubbles, which contain chambers. The object placed for its emergence from the prebiotic world four billion years ago? scale is two centimeters across. These fossil chimneys were formed well after life’s origin, but may be similar to those in which, according to one The short answer is that they can’t, yet. -
Life As a Guide to Prebiotic Nucleotide Synthesis
COMMENT DOI: 10.1038/s41467-018-07220-y OPEN Life as a guide to prebiotic nucleotide synthesis Stuart A. Harrison1 & Nick Lane 1 Synthesis of activated nucleotides has been accomplished under ‘prebiotically plausible’ conditions, but bears little resemblance to the chemistry of life as we know it. Here we argue that life is an indispensable guide to its own origins. 1234567890():,; “The justification of prebiotic syntheses by appealing to their similarity to enzymatic mechanisms has been routine in the literature of prebiotic chemistry. Acceptance of the RNA World hypothesis invalidates this type of argument. If the RNA World originated de novo on the primitive Earth, it erects an almost opaque barrier between biochemistry and prebiotic chemistry.” Leslie Orgel 2004. There is little doubt that RNA is central to the origins of genetic information and protein synthesis, but that is a far cry from the stronger statement, articulated by Orgel, that if metabolism arose from an RNA world, then life can give no insights into its own origin1. Yet this view resonates with much prebiotic chemistry over the last decade. Activated pyrimidine and oxopurine nucleotides have been synthesised at good yield from purportedly prebiotically plausible precursors such as cyanide and cyanoacetylene, driven by UV radiation2. Wet-dry cycles in the presence of laminated clay minerals and lipids can polymerise nucleotides to RNA3. Accordingly, some claim that the problem has already been solved, at least conceptually. Has it? Not in everybody’s view. Perhaps the biggest problem is that the chemistry involved in these clever syntheses does not narrow the gap between prebiotic chemistry and biochemistry—it does not resemble extant biochemistry in terms of substrates, reaction pathways, catalysts or energy coupling4. -
10 Metabolism
Route to life by chemical networks P. L. Luisi Mol Syst Biol. 2014, 10, 729 Metabolism-first vs. Genes-first Genetics/replication-first: an information-carrying polymer capable of replication (RNA or something simpler) spontaneously arose from available prebiotic molecules available on early Earth. Metabolism incorporated later as a mean to receive energy from the surroundings in a controlled manner. Metabolism-first: primitive metabolic cycles spontaneously assembled from simple prebiotic organic molecules or inorganic carbon sources as CO2. And the cycles produced a set or more or less complex molecules needed for the replication process and construction of the genetic apparatus. The supposed proto-metabolism would differ from the currently known one, because the chemical reactions were not catalysed by efficient enzymes, nor were aminoacid and peptide sequences determined by DNA. The involved reactions were either spontaneous, or catalysed by inorganic catalysts or peptides. Inorganic catalysts would be molecules, or ions, in solutions or on surfaces of solids such as clays or pyrites. Peptides (or peptoids) formed either by random oligomerization or mutual catalysis. Metabolism and self-organization of chemical networks One of pre-conditions for life is to be far from thermodynamic equilibrium. Life uses non-linear effects to amplify and stabilize minor environmental effects Spatial and temporal synchronisation of reactive processes provides molecules with patterns of collective behavior. Under certain conditions far from thermodynamic equilibrium, heterogenous mixtures can trigger emergent properties at the collective level. Oscilatory and autocatalytic processes are very common in biological systems. Examples include: metabolic cycles, immune response, or apoptosis. Oscilatory reactions – importance for homeostasis. -
Meetings and Positions Classified Cb Current Biology
MEETINGS AND POSITIONS CLASSIFIED CB CURRENT BIOLOGY Section includes advertisements for announcements of meetings, positions, or other related events. Classified Advertising Closing Dates Price Structure: 1995 rates are $200/£320 for a quarter page, $300/£480 tot a And Bonus Distribution half page, and $500/£800 for a full page. Discounts are offered on ads placed in more than one Current Biology Ltd. journal. Rates for colottr advertisements are Issue Deadline given upon request. Rates are non-commissionable. September August 7, 1995 October September 8, 1995 Ad Size: All materials must follow the following ad dimensions. A quarter page November October 9, 1995 ad: 3.346" by 4.685" or 85mm by 119mm; a half page ad: 6.85" by 4.685" or 174mm by 119mm (horizontal); 3.346" by 9.528" or 85mm by 242mm (vertical); a December November 7, 1995 full page ad 6.85" by 9.528"or 174mm by 242mm. Current Biology offers typeset- Januai"y 1996 December 7, 1995 ting at no additional charge. The size of all ads typeset by Current Biology will be determined by the number of words in the copy. A quarter page contains up to Current Biology offers bonus distribution at 150 words, a half page contains tip to 250 words, and a fnll page contains up to several meetings and symposia 500 words. throughout the year. Mechanical Requirements: All classified advertising that is not typeset by For more information please call for a Current Biology must be received in one of the following forms: electronically on classified advertising media kit. -
Prebiotic Chemistry and the Origin of the RNA World
Critical Reviews in Biochemistry and Molecular Biology, 39:99–123, 2004 Copyright c Taylor & Francis Inc. ISSN: 1040-9238 print / 1549-7798 online DOI: 10.1080/10409230490460765 Prebiotic Chemistry and the Origin of the RNA World Leslie E. Orgel The Salk Institute, La Jolla, California, USA a “chicken and egg problem” and to ask which came first, The demonstration that ribosomal peptide synthesis is a proteins or nucleic acids? At the time, it was well recog- ribozyme-catalyzed reaction makes it almost certain that there was nized that natural selection through replication and muta- once an RNA World. The central problem for origin-of-life studies, tion was the only mechanism for evolving complex bio- therefore, is to understand how a protein-free RNA World became chemical systems from simpler ones. Trying to solve the established on the primitive Earth. We first review the literature on “chicken and egg” problem, therefore, was equivalent to the prebiotic synthesis of the nucleotides, the nonenzymatic synthe- asking whether proteins or nucleic acids were more plausi- sis and copying of polynucleotides, and the selection of ribozyme ble as the components of a self-contained replicating sys- catalysts of a kind that might have facilitated polynucleotide repli- tem. The answer seemed obvious: nucleic acids. Watson- cation. This leads to a brief outline of the Molecular Biologists’ Crick base-pairing provided a very plausible mechanism Dream, an optimistic scenario for the origin of the RNA World. In by which a polynucleotide could direct the synthesis of the second part of the review we point out the many unresolved problems presented by the Molecular Biologists’ Dream.