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WU095-FM WU095/Kulaev March9,2004 15:47 CharCount=0 The Biochemistry of Inorganic Polyphosphates i WU095-FM WU095/Kulaev March9,2004 15:47 CharCount=0 ii WU095-FM WU095/Kulaev March9,2004 15:47 CharCount=0 The Biochemistry of Inorganic Polyphosphates Second Edition I S Kulaev Moscow State University, Moscow, Russian Federation and G K Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation V M Vagabov and T V Kulakovskaya G K Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation iii WU095-FM WU095/Kulaev March9,2004 15:47 CharCount=0 Copyright(cid:1)C 2004 JohnWiley&Sons,Ltd,TheAtrium,SouthernGate Chichester,WestSussex,PO198SQ,England Phone (+44)1243779777 Email(forordersandcustomerserviceenquires):[email protected] VisitourHomePageonwww.wiley.co.ukorwww.wiley.com AllRightsReserved.Nopartofthispublicationmaybereproduced,storedinaretrievalsystemortransmittedin anyformorbyanymeans,electronic,mechanical,photocopying,recording,scanningorotherwise,exceptunder thetermsoftheCopyrightLicensingAgencyLtd,90TottenhamCourtRoad,LondonW1P0LP,UK,without thepermissioninwritingofthePublisher.RequeststothePublishershouldbeaddressedtothePermissions DepartmentJohnWiley&Sons,Ltd,TheAtrium,SouthernGate,Chichester,WestSussex,PO198SQ,England, [email protected],orfaxedto(44)1243770620. Thispublicationisdesignedtoprovideaccurateandauthoritativeinformationinregardtothesubjectmatter covered.ItissoldontheunderstandingthatthePublisherisnotengagedinrenderingprofessionalservices.If professionaladviceorotherexpertassistanceisrequired,theservicesofacompetentprofessionalshouldbe sought. OtherWileyEditorialOffices JohnWiley&Sons,Inc.111RiverStreet,Hoboken,NJ07030,USA Jossey-Bass,989MarketStreet,SanFrancisco,CA94103-1741,USA Wiley-VCHVerlagGmbH,Pappellaee3,D-69469Weinheim,Germany JohnWiley&SonsAustralia,Ltd,33ParkRoad,Milton,Queensland,4064,Australia JohnWiley&Sons(Asia)PteLtd,2ClementiLoop#02-01,JinXingDistripark,Singapore129809 JohnWiley&SonsCanadaLtd,22WorcesterRoad,Etobicoke,Ontario,Canada,M9W1L1 Wileyalsopublishesitsbooksinavarietyofelectronicformats.Somecontentthatappearsinprintmaynotbe availableinelectronicbooks. LibraryofCongressCataloging-in-PublicationData Kulaev,I.S.(Igor’Stepanovich) Thebiochemistryofinorganicpolyphosphates/I.S.Kulaev,V.M. Vagabov,T.V.Kulakovskaya.—2nded. p. ; cm. Includesbibliographicalreferencesandindexes. ISBN0-470-85810-9(cloth) 1.Polyphosphates—Metabolism. 2.Polyphosphates—Physiologicaleffect. [DNLM: 1.Polyphosphates—metabolism. 2.Enzymes—metabolism.QV 285K96b 2004] I.Vagabov,V.M. II.Kulakovskaya,T.V. III.Title. QP535.P1 K84 2004 572(cid:2).514—dc22 2003025236 BritishLibraryCataloguinginPublicationData AcataloguerecordforthisbookisavailablefromtheBritishLibrary ISBN0470858109 Typesetin10/12pt.TimesbyTechBooks,NewDelhi,India PrintedandboundinGreatBritainbyMPG,Bodmin,Cornwall Thisbookisprintedonacid-freepaperresponsiblymanufacturedfromsustainableforestry inwhichatleasttwotreesareplantedforeachoneusedforpaperproduction. iv WU095-FM WU095/Kulaev March9,2004 15:47 CharCount=0 To the respected memory of Andrei Nikolaevich Belozersky, an outstanding scientist, teacher and man v WU095-FM WU095/Kulaev March9,2004 15:47 CharCount=0 vi WU095-FM WU095/Kulaev March9,2004 15:47 CharCount=0 CONTENTS ForewordtotheFirstEdition xi Preface xiii Acknowledgements xv Introduction 1 1 TheChemicalStructuresandPropertiesofCondensed InorganicPhosphates 3 1.1 TheStructuresofCondensedPhosphates 3 1.1.1 Cyclophosphates 4 1.1.2 Polyphosphates 5 1.1.3 BranchedInorganicPhosphates,or‘Ultraphosphates’ 7 1.2 SomeChemicalPropertiesofCondensedInorganicPolyphosphates 9 1.3 Physico-ChemicalPropertiesofCondensedInorganic Polyphosphates 12 2 MethodsofPolyphosphateAssayinBiologicalMaterials 15 2.1 MethodsofExtractionfromBiologicalMaterials 15 2.2 ChromatographicMethods 17 2.3 ColorimetricandFluorimetricMethods 20 2.4 CytochemicalMethods 22 2.5 X-RayEnergyDispersiveAnalysis 24 2.6 31PNuclearMagneticResonanceSpectroscopy 26 2.7 OtherPhysicalMethods 31 2.8 GelElectrophoresis 31 2.9 EnzymaticMethods 33 vii WU095-FM WU095/Kulaev March9,2004 15:47 CharCount=0 viii Contents 3 TheOccurrenceofPolyphosphatesinLivingOrganisms 37 4 TheFormsinwhichPolyphosphatesarePresentinCells 45 4.1 Polyphosphate–CationComplexes 45 4.2 Polyphosphate–Ca2+–PolyhydroxybutyrateComplexes 46 4.3 ComplexesofPolyphosphateswithNucleicAcids 46 4.4 BindingofPolyphosphateswithProteins 50 5 LocalizationofPolyphosphatesinCellsofProkaryotes andEukaryotes 53 5.1 Prokaryotes 53 5.2 Eukaryotes 55 6 EnzymesofPolyphosphateBiosynthesisandDegradation 65 6.1 EnzymesofPolyphosphateBiosynthesis 65 6.1.1 Polyphosphate Kinase (Polyphosphate:ADP Phosphotrans- ferase,EC2.7.4.1) 65 6.1.2 3-Phospho-D-Glyceroyl-Phosphate:Polyphosphate Phospho- transferase(EC2.7.4.17) 70 6.1.3 Dolichyl-Diphosphate:PolyphosphatePhosphotransferase (EC2.7.4.20) 71 6.2 EnzymesofPolyphosphateDegradation 73 6.2.1 Polyphosphate-GlucosePhosphotransferase(EC2.7.1.63) 73 6.2.2 NADKinase(ATP:NAD2(cid:1)-Phosphotransferase,EC2.7.1.23) 75 6.2.3 Exopolyphosphatase (Polyphosphate Phosphohydrolase, EC 3.6.1.11) 75 6.2.4 Adenosine–TetraphosphatePhosphohydrolase(EC3.6.1.14) 85 6.2.5 Triphosphatase(Tripolyphosphatase,EC3.6.1.25) 85 6.2.6 Endopolyphosphatase (Polyphosphate Depolymerase, EC 3.6.1.10) 86 6.2.7 PolyP:AMPPhosphotransferase 87 7 TheFunctionsofPolyphosphatesandPolyphosphate- DependentEnzymes 91 7.1 PhosphateReserve 91 7.1.1 InProkaryotes 92 7.1.2 InEukaryotes 93 7.2 EnergySource 94 7.2.1 PolyphosphatesinBioenergeticsofProkaryotes 94 7.2.2 PolyphosphateinBioenergeticsofEukaryotes 95 WU095-FM WU095/Kulaev March9,2004 15:47 CharCount=0 Contents ix 7.3 CationsSequestrationandStorage 97 7.3.1 InProkaryotes 97 7.3.2 InEukaryotes 97 7.4 ParticipationinMembraneTransport 99 7.5 CellEnvelopeFormationandFunction 103 7.5.1 PolyphosphatesintheCellEnvelopesofProkaryotes 103 7.5.2 PolyphosphatesintheCellEnvelopesofEukaryotes 104 7.6 RegulationofEnzymeActivities 106 7.7 GeneActivityControl,DevelopmentandStressResponse 108 7.7.1 InProkaryotes 108 7.7.2 InLowerEukaryotes 115 7.8 TheFunctionsofPolyphosphatesinHigherEukaryotes 118 8 ThePeculiaritiesofPolyphosphateMetabolisminDifferent Organisms 125 8.1 Escherichiacoli 125 8.1.1 TheDynamicsofPolyphosphatesunderCultureGrowth 125 8.1.2 TheEffectsofP LimitationandExcess 127 i 8.1.3 The Effects of Mutations on Polyphosphate Levels and Polyphosphate-MetabolizingEnzymeActivities 129 8.1.4 TheEffectsofNutritionDeficiencyandEnvironmentalStress 131 8.2 Pseudomonasaeruginosa 131 8.3 Acinetobacter 134 8.4 Aerobacteraerogenes(Klebsiellaaerogenes) 135 8.5 Azotobacter 137 8.6 Cyanobacteria(Blue–GreenAlgae)andotherPhotosynthetic Bacteria 138 8.7 MycobacteriaandCorynebacteria 140 8.8 Propionibacteria 142 8.9 Archae 145 8.10 Yeast 147 8.10.1 YeastCellsPossessDifferentPolyphosphateFractions 147 8.10.2 TheDynamicsofPolyPFractionsduringtheCellCycle 148 8.10.3 TheRelationshipbetweentheMetabolismofPolyphosphates andotherCompounds 150 8.10.4 Polyphosphate Fractions at Growth on a P-Sufficient i MediumwithGlucose 150 8.10.5 TheEffectsofP LimitationandExcess 153 i 8.10.6 TheEffectsofotherConditionsonthePolyphosphate ContentinYeastCells 157 8.10.7 The Effects of Inhibitors on the Polyphosphate Content in YeastCells 160 8.10.8 TheEffectsofMutationsontheContentandChainLengths ofPolyphosphateinYeast 162