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Acetate Metabolism in Methanothrix Soehngenii

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Acetate Metabolism in Methanothrix Soehngenii ACETATE METABOLISM IN METHANOTHRIX SOEHNGENII CENTRALE LANDBOUWCATALOGUS 0000 0456 8685 Promotor: Dr. A.J . B. Zehnder, hoogleraar in de microbiologic Co-promotor: Dr. Ir. A.J . M. Stams universitair docent bij devakgroe p microbiologic M. S. M. Jetten Acetate metabolism in Methanothrix soehngenii Proefschrift ter verkrijging van de graad van doctor in de landbouw- en milieuwetenschappen op gezag van de rector magnificus, Dr. H. C. van der Plas, in het openbaar te verdedigen op vrijdag 20 december 1991 des namiddags te vier uur in de aula van de Landbouwuniversiteit te Wageningen. LAIN'DBOUWUNIVEuSIXED I WAGEMNGEN Dit promotie onderzoek werd uitgevoerd binnen het Innovatief Onderzoeks Pro- gramma biotechnologie (IOP-b) en begeleid door de Programma Commissie Industriele Biotechnologie van het Ministerie van Economische Zaken. De afronding van de promotie werd tevens mogelijk gemaakt door bijdrages van het LEB Fonds, de Landbouwuniversiteit en de vakgroep Microbiologic X N0l70't >V6> Stellingen 1. Het meten van complexe enzymreacties in cel-vrije extracten levert meer interpretatieproblemen, dan uitkomsten op. Fisher, R. and Thauer, R.K. (1988) Methanogenesis from acetate in cell extracts ofMethano- sarc'ma barken.Arch . Microbiol. 151, 459-465. 2. De bevinding van Fiala en Stetter, dat Pyrococcus furiosus alleen H2 en C02 als eindprodukten maakt, berust op onzorgvuldige analyse metho- den. Fiala, G. and Stetter, K.O (1986) Pyrococcus furiosus sp. nov. represents a novel genus of marine heterotrophic archaebacteria growing optimally at 100°C. Arch. Microbiol. 145, 56-61. 3. Het "herontdekken" van het gave=1.87 signaal in EPR spectra van het CO dehydrogenase van Clostridium thermoaceticum door Lindahl et. al. getuigt niet van veel bekendheid met eigen onderzoek. Lindahl, P.A., Munck, E. and Ragsdale, S.W. (1990) CO dehydrogenase from Clostridium thermoaceticum. J. Biol. Chem 265,3873-3879 . Ragsdale, S.W, Ljungdahl, L.G and DerVartanian, D.V. (1982) EPR evidence for nickel- substrate interaction in carbon monoxide dehydrogenase from Clostridium thermoaceticum. Biochem. Biophys. Res. Comm.108, 652-663. 4. De bewering van Kohler dat Methanothrix soehngenii "sich wenig eignet als biochemisches Untersuchungsobjekt" wordt door dit proefschrift teniet gedaan. Kohler, H.-P.E. (1986) Acetatkatabolismus in Methanothrix soehngenii. Dissertatie ETH Zurich no. 8033, p. 92. Dit proefschrift. 5. Resultaten, verkregen door het gebruik van P1,P5-Di(adenosine-5')pen- tafosfaat als remmer voor adenylaat kinase in gekoppelde enzym assays, dienen uiterst zorgvuldig ge'interpreteerd te worden. Van Groenestijn, J.W., Bentvelsen, M.M.A., Deinema, M.H. and Zehnder, A.J.B. (1989) Polyphosphate-degrading enzymes in Acinetobacter spp. and activated sludge. Appl.Environ. Microbiol. 55, 219-223. 6. In experimenten waarbij de hoeveelheid azijnzuur in grammen wordt afgewogen, is het gebruik van de "eenheid" mg COD (Chemical Oxygen Demand) als maat voor de hoeveelheid azijnzuur niet op zijn plaats. Ten Brummeler, R, Hulshoff Pol, L.W., Dolfmg, J., Lettinga, G. and Zehnder, AJ.B. (1985) Methanogenesis in an UASB reactor at pH 6 on an acetate-propionate mixture. Appl. Environ. Microbiol. 49, 1472-1477. 7. Stellingen bestel je bij Overtoom. 8. Het aantal publicaties per WP-er is omgekeerd evenredig met het aantal WP-ers per vakgroep. Wetenschappelijk Jaarverslag 1989, Landbouw Universiteit Wageningen. 9. Bij het gebruik van de MPN methode zit men er waarschijnlijk Meestal Pijnlijk Naast. 10. Het houden van een evaluatie heeft alleen (positief) effect, wanneer zowel de gever als ontvanger op de hoogte zijn van de grondregels van evalueren. 11. De grafieken, die in de media gebruikt worden om de belangrijkste beursparameters weer te geven, dragen niet bij aan een beter begrip van deze parameters. 12. Stakingen in het openbaar vervoer treffen in het algemeen de verkeer- de doelgroep. Stellingen behorende bij het proefschrift "Acetate metabolism in Methanothrix soehngenii" van M.S.M. Jetten. Wageningen 20 december 1991 CONTENTS Chapter Titel 1 General introduction 1 2 Acetate threshold values and acetate activating enzymes in 17 methanogenic bacteria. 3 Isolation and characterization of acetyl-CoA synthetase from 25 Methanothrix soehngenii. 4 A fluoride-insensitive inorganic pyrophosphatase isolated 33 from Methanothrix soehngenii. 5 Adenine nucleotide content and energy charge of 45 Methanothrix soehngenii during acetate degradation. 6 Purification and characterization of an oxygen stable carbon 53 monoxide dehydrogenase of Methanothrix soehngenii. 7 Paramagnetic centers and acetyl-coenxzyme A / CO exchange 61 activity of carbon monoxide dehydrogenase from Methanothrix soehngenii 8 EPR characterization of a high spin system in carbon 71 monoxide dehydrogenase from Methanothrix soehngenii 9 Purification and some properties of the methyl-CoM 87 reductase of Methanothrix soehngenii 10 Discussion and summary 93 Discussie en samenvatting Publication List 104 Nawoord 105 Curriculum Vitae 106 Chapter 1 General Introduction GENERAL INTRODUCTION Preview as nitrate or sulfate terminal degradation steps are performed by the methane bacteria In this chapter the reader will be introduced [8]. In this step the methane bacteria con­ to the main aspects of the methane vert Hj/C02 and acetate to methane [1,8]. formation from acetate. In the first part the The methane bacteria play an important position of methanogenesis in the anaerobic regulatory role in the proton and electron degradation of organic matter is described. flow during the anaerobic degradation of Thereafter a brief summary of the main organic matter [7,8]. The comsumption of characteristics of the methane bacteria will hydrogen provides a low partial hydrogen be given. This summary is followed by a pressure. This enables the obligate proton- historical overview of methanogenesis from reducing bacteria to degrade the organic acetate. Then an overview of the physiology acids, which are thermodynamically very un­ and biochemistry of the acetoclastic methan­ favourable reactions [7-10]. The com­ ogenesis is given. At the end of the intro­ sumption of acetate by the acetoclastic duction a short summary of the data availa­ methanogens prevents acidification of the ble on the molecular biology of Methanothrix anaerobic ecosystem [11]. and an outline of this thesis are presented. Acetate is quantitatively the most important intermediate in the anaerobic degradation of organic matter [11,12]. It is the most abun­ Methanogenesis dant precursor of methane formation. Seventy precent of the methane in anaerobic Microorganisms play an important role in digestors is derived from acetate [13]. In the conversion of organic and inorganic sediments, flooded soils and rice-fields also matter [1]. Under anaerobic conditions 60-80 % of the methane is formed from organic matter is degraded by the acetate [3,14-17]. Further the conversion cooperative interaction of several different rate of acetate by methanogenic bacteria is physiological groups of micro-organisms proposed to be the rate limiting step in the [2-4]. A schematic presentation of the degradation of soluble organic matter under anaerobic degradation under methanogenic anaerobic conditions [18]. The study of conditions is depicted in Fig. 1. The acetoclastic methanogens, therefore, is of anaerobic degradation of organic matter relevance to our understanding of anaerobic starts with the hydrolysis of complex processes and their optimal application in biopolymers into the corresponding treatment of waste water from various monomers by fermentative bacteria [5,6]. sources. These monomeric products (sugars, fatty acids and amino acids) are converted by fermentative bacteria to intermediate Methanogenic bacteria products like, acetate, propionate, butyrate, lactate and alcohols [7]. Most of these com­ Methanogenic bacteria have been isolated pounds are oxidized by obligate proton- from nearly every habitat in which anaerobic reducing acetogenic bacteria to acetate, degradation of organic material takes place, hydrogen and C02 [7]. such as waste water digestors, fresh water In the absence of light or electron acceptors and marine sediments, and intestinal tracts complex biopolymers PROTEINS CARBOHYDRATES LIPIDS h 1 Ji AMINO ACIDS SUGARS FATTY ACIDS 2 2 INTERMEDIARY PRODUCTS 2 PROPIONATE BUTYRATE / 3 \ ' ' 1r ACETATE 4 HYDROGEN X / 5 / 5 y METHANE Fig. 1: Anaerobic degradation of soluble organic matter under methanogenic conditions (1): Hydrolytic degradation of biopolymers (2): Fermentation of monomers (3): Oxidation byobligat e proton reducing bacteria (4): Acetogenic hydrogen conversion (5): Methanogenesis of man and animals [20-24]. Historic overview of the methane formation axonomically, methane bacteria comprise of from acetate a rather diverse group. Balch et al. proposed classification into three orders and six fami­ After the discovery of methane (aria lies on the basis of morphological differen­ infiammabile) by A. Volta in 1776, it took ces : Methanobacteriales (Methanobacteria- another century before the microbial origin ceae and Methanothermoceae), Methano- of the methane formation from coccales (Methanococceae) and Methano- decomposing plant material was microbiales (Methanomicrobiaceae, demonstrated by Bechamp (1868) and Methanosarcinaceae and Methanopla- Popoff (1873) [41-43]. The methane naceae) [25]. Although, taxonomically rather production from acetate was firstly described diverse, the methane bacteria were by Hoppe-Seyler in 1876 [44]. Even before reorganized
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