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Nitrogen Assimilation and Energy Conservation in Nitrosomonas

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Nitrogen Assimilation and Energy Conservation in Nitrosomonas WAITT, INSTITUTE þ.4-8+ LIBRARY NITROG EN ASSII{ILATION AND ENERGY CONSERVATION IN ¡VT?ROSOþIONAS EUROPAEA AND NT?ROBACTER AGILTS by Sharad Kumar, M.Sc. A thesis submitted in fulfilment of the requirements for the degree of Doctor of PhiTosoPhY Department. of AgriculÈural Biochemistry, l,laite Agricultural Research Institute' The University of Adelaide. -x- October, 1983. l_ PREFACE Part of the work described in this thesis has been presented in scientific meetings (Australian Biochemical Society, 1981' 1983; X.II International Congress of Biochemistry, L982). Some of the results have been published or submitted for publication in the journals listed below: 1). Oxygen-dependent nitrite uptake and nitrate production in cells, spheroplasts and membrane vesicles of iVj¿robacter agiTis. S. Kumar and D.J.D. Nicholas FEMS MicrobioT. Lett. 11: 202-206 (1981). 2). The uptake of nitrite and oxygen and the production of nitrate by cells, spheroplasEs and vesicles of Ni trobacter agiTis. S. Kumar and D.J.D. Nicholas Proc. Aust. Biochen. Soc. I4z 48 (1981). 3). Assimilation of inorganic nitrogen compounds by tVitrobacter agiTis. S. Kumar and D.J.D. Nicholas J. Gen. MicrobioT. 128: 1795-1801 (1982). 4). RespiraÈion-dependent proton transloction in NiÈrosononas europaea and its apparent absence in Nitrobacter agiTis during inorganic oxidations. T.C. Hollocher, S. Kumar and D.J.D. Nicholas J. BacterioT. I49z 1013-1020 (1982). 5). A proton-moÈive force dependent adenosine-5t-triphosphate synthesis in spheroplasts of Nitrosononas europaea. S. Kumar and D.J.D. Nicholas FEMS MicrobioT. Lett. l4z 2I-25 (1982). 6). ATP biosynthesis in the niÈrifying bacterium Nitrosomonas eurapaea; S. Kumar and D.J.D. Nicholas Abstracts of 12th InternaËiona7 Congress of Biochemistry, Perth, p.299 (1982) 7). The proton-elecÈrochemical gradienEs in washed cel1s of IVitrosononas europaea and Nitrobacter agilis. S. Kumar and D.J.D. Nicholas J. BacterioT. I54z 65-71 (f983). 1l_ 8). Definitivu 15N-NMR evidence that water serves as a source of tgt durì-ng nitrite oxidation by Nitrobacter agiTis. S. Kumar, D.J.D. Nicholas and E.J. Williams FEBS Lett. l52z 7l-74 (1983). 9). Adenylylation and deadenylylation of gluËamine synthetase in the niÈrifying bacteria Nitrosomonas europaea and Nitrobacter agiTis, S. Kumar and D.J.D. Nicholas Proc. Aust. Biochen. Soc. 15: 56 (1983). 10). Purification, properLies and regulation of glut.amine synt.hetase from Ni:robacter agilis. S. Kumar and D.J.D. Nicholas J. Gen. MicrobioT. Submitted for publication. l1). NAD+ and NADP+ dependent glutamate dehydrogenases in Nitrobacter àgi7is. S. Kumar and D,J.D. Nicholas J. Gen. MicrobioT. Submitted for publication. II 12). Na- and K- transport in Nitrosononas europaea and Nitrobacter agiTis. S. Kumar and D.J.D. Nicholas Biochin. Biophys. Acta. SubmiÈted for publication. l_11_ ACKNO\^ILEDGEI"IENTS I record my deep and sincere Èhanks to my supervisor, professor D.J.D. Nicholas, Chairman of the Department of Agricultural Biochemistry, Llaite Agricultural Research Institute, The University of Adelaide, for his guidance, constant encouragenent and consÈrucLive criticism throughout the progress of the present investigation and the preparaÈion of this manuscript. I would also like to thank Drs. M.E. Tate and T.C. Hollocher for helpful suggestions, Eechnical advice and critical discussions during the course of present investigation and to Dr. E.H. hlilliams for the help w-ith NMR spectroscopy. Thanks are due to Mr. R.G; Batt for reading the draft of this manuscript, Mr. B.A. Palk for preparing Èhe photographic prints, Mrs. M. Brock for skillful typing and to all others who helped me from time to tine. The award of U.R.G. scholarship by The University of Adelaide is gratefully acknowledged- 1V DECLARATION I hereby declare that thÏs thesis contains no naterial which has been accepted for the award of any other degree or diplorna in any university. To the best of my knowledge and belief, no naterial described herein has been previously published or written by another person except when due reference is nade in the text. If accepted for the award of a Ph,D. degree, this thesis will be available for loan and photocopying. SHARAD KUMAR. NOMENCULATURE AND ABBREVIATI ONS The major enzymes mentioned in this thesis are listed below with their numbers and systematic names as recommended by Enzyme Commission (Enzyme nomenculature I97B). Trivial Name E.C. Name and Number Adenosine triphosphatase (ATPase) ATP phosphohydrolase E.C. 3.6.1.3 Glutamate dehydrogenase (GDH) L-gluLamate : NAD(P)+ oxidoreductase ( deaminating ) NAD+-GDH E.C. I.4.r.2 NAD(P)+-cDH E.C. 1.4.1.3 NADPï-GDH E.C. r.4.r.4 Glutamate synthase (GOGAT) L-glutamate : NAD+ oxidoreductase ( transaminating ) E.C. r.4.r.14 Glutamine synthetase (GS) L-glut.amate : ammonia ligase (ADP forming) E.C.6.3.r.2 The abbreviations for chemicals, symbols and units in general follow either the tentaÈive rules of IUPAC-IUB Commission on Biochemical Nomenculature (Biochen. J. (1966) 101: 1-7) or the Instruction to Authors for the Biochinica et Biophysica Acta (BBA (1982) 7l5z l-23). Chemicals ADP adenosine 5r-diphosphate | AMP adenosine 5 -monophosphate ATP adenosine 5t-triphosphate BSA bovine serum albumin cccP carbonyl cyanide rn-chlorophenyl hydrazone CDP cytidine 5t-diphosphate CMP cytidine 5r-monophosphate CTAB cetyl trimethyl ammonium bromide CTP cytidine 5t-triphosphate DBP 2.4 dibromophenol t DCCD N, N dicyclohexylcarbodiimide DESB diethylstilbestrol DIECA diethyl dithiocarbamate (sodium salt) 2,4 DNP 2.4-dinitrophenol DBP 2 .4-dibromophenol v1 Chemicals continued/. BDTA ethylenediamine tetra acetic acid Y-GH .¡-glutamyl hydroxamate | GDP guanosine 5 -diphosphate t GMP guanosine 5 -monophosphate GTP guanosine 5t-triphosphaEe HEPES 4- (Z-hy droxyethyl ) -1 -piperazine-eLhanesul phonic acid H0QN0 2-hept.yl-4-hydroxy quinoline-N-oxide 8-HQ 8-hydroxy quinoline IDP . ionosine 5t-diphosphate I IMP ionosine 5 -monophosphate ITP ionosine 5r-triphosphate MSX L-methionine-DL-su1 phoximine _J- NAD. nicotinamide-adenine dinucleotide (oxidised) NADH nicot,inamide-adenine dinucleoti de (reduced) NADP+ nicotinamide-adenine dinucleotide phosphate (oxidised) NADPH nicotinamide-adenine dinucleotide phosphate (reduced) NBD-chloride 4-chloro-7-nitrobe nzo-Z-oxa-1, 3-diazole NEM N-ethyl-maleimide N-serve 2-chloro-6-trichloromethyl pyridine pCl4B p-chloro mercuribenzoaLe PCP penta chlorophenol POPOP 1,4 bis (2,(4 methyl-5-phenyl oxazolyl)) benzene PPO 2r5 diphenyloxazole SDS sodium-dodecylsulf ate TCA trichloroacetic acid t- lMP thymidine 5 monophosphate 2-TMP 2-t,richloromethyl pyridine TPB tetra phenyl boron Tris 2-amino-2-hydroxymethyl propane-1' 3-diol TPMP+ t.riphenyl methyl phosphosphonium cation J. TPP. teEra-phenyl phosphonium cation TTP thymidine 5r-triphosphate UDP uridine 5r-diphosphate t TIMP uridine 5 -monophosphate UTP uridine 5t-triphosphate VI]. Symbols and Units A absorbance amu atomic mass unit "c degree centrigrade (celcius) I,I curie cm centlm6ter d day(s) Ap or ür+ proton-motive force or proton-electrochemical gradient apH transmembrane pH gradient Aü transmembrane potenLial difference (membrane potential) F free energy or Faradayrs constant ëo unit of gravitational field èo gram G Gibbfs energy constant h hour(s) *tt+/0 no. of protons translocated per 2e- Eransferred to 0 Hz hertz J joule(s ) k kilo K equilibrium constant kcycle kilo cycle K. inhibitor constanÈ I KJ kilojoules K Michaelis constant m KsoI solubility constanÈ KV kilo volt ì. wave length 1 litre M molar m meter mCi nillicurie mg milligram uci microcurie min rninute(s) m1 millilitre mmol millimole ( s ) mM millimolar ug microgram v11l_ ul microlitre Þrnol miçromole ( s ) Ul"I micronolar N normal nm nanometer nmol nanamole ( s ) 7" percent Pi ilorganic phosphate pHe extracellular pH pHi intracellular pH R gas constant S second ( s ) S substrate concentration t time rà half time T thermodyamic Lemperature (Kelvin) v volume v velociEy of the reaction Vmax rate of enzyme catalysed reaction aÈ infinite concentration of substrate wt weight 0thers approx. approximately atm. atmosphere conc. concentration cpm counts per minute e. g. for example et a7. et aTia (and others) a GC/MS gas chro'matography linked to mass-sPectrometry a. e. that is max. maximum min. minimum IIt-t p-t 0= neta-r pâra-¡ ortho- Nl"fR nuclear magneËic resonance No. number / per p. (plural pp.) page PAGE Polyacrylamide gel electrophoresis S.D. standard deviation l-x Others continued/. S.E.M. standard error of means soln. solution / temp. temperature Viz. namely Vs. versus v/v volume : volume w/v weight : volume less than less Fhan or equal to greater Lhan greater than or equal to approximately equal TABLE OF CONTENTS x TABLE OF CONTBNTS Page No. PREFACE i ACKNOI,ILEDGEMENTS )-aI DECLARATION iv NOMENCULATURE AND ABBREVIATIONS v TABLE OF CONTENTS x LIST OF TABLES xv LIST OF FIGURES xviii SUMMARY xxii 1. INTRODUCTION 1 1.1 NITRIFYING BACTERIA I 1.1.1 Morphology 1 r.t.2 The concept of chenoTithotrophy 1 1.1.3 Amnonia and hydroxyTanine oxidation by Nitrosomonas 3 1.1.3.1 Ammonia Oxidation 3 1.1.3.2 Hydroxylamine Oxidation 5 1.1 .4 Nitrite oxidation by Nitrobacter agiTis I 1.1 .5 Energy coupTing 10 1.1.5.1 Nitrosononas species 10 L.L.5.2 Nitrobacter species I2 1.1.6 Nitrogen assiniTation' I4 T.2 AIMS OF THE STUDY 15 2. I"ÍATERIALS AND METHODS 17 2.7 MATERIALS 2.T.L ChenicaT and biochenicaTs T7 2.t.2 StabTe isotopes 77 2.r.3 Radioisotopes 18 2.r.4 SoTutions, buffers and solvents 18 2.t.5 Chronatographic naterial s 18 2.r.6 Enzynes and marker proteins 19 2.L.7 BacteriaT cuTtures I9 2.2 METHODS I9 2.2.r Growth and harvesting the bacteria 19 2.2.2 Preparation of spheropTasts and nenbrane vesicles 20 2.2.3 Preparation of cel,l-freet'N extracts 20 2.2.4 Incorporation of 7ub"77ed conpounds into ce71 nitrogen 2O 2.2.5 Enzyne purification 2I xl- Paee No.
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