Biology of the Prokaryotes PDF
Preview Biology of the Prokaryotes
Biology of the Prokaryotes Biology of the Prokaryotes Edited by Joseph W. Lengeler, Gerhart Drews and Hans G. Schlegel © 1999 Georg Thieme Verlag, Rüdigerstrasse 14, D-70469 Stuttgart, Germany. ISBN: 978-0-632-05357-5 Biology of the Prokaryotes Edited by Joseph w. Lengeler Gerhart Drews Hans G. Schlegel UniversityofOsnabrOck UniversityofFreiburgfBr. UniversityofGottingen 940illustrations 150tables I b Thieme Stuttgart Blackwell NewYork 1999 Sci"ence UbnuyofCongnuColO1<Jl/ng·/n·PIl_donDolO Biologyoftheprolc.1ryotesI~itedbyJosephW.lengeler.Cer haltDrews,HansG.SChlegel. p. em Includesbibliographical referencesand index. ISBN3-13-108411-1. 1.Prokaryotes.1.Lengeler.Josephw.n.Drews, GerhartIII.SChlegel.HansGOnter.1924- (DNLM: 1.ProkaryoticCelis-physiology.2.Bacteria. QW5100151999) QJl41.2.B55 199 579.3-dc21 DNW/DLC forUbraryofCongress 98-36569 CIP 01999GeorgThiemeVerlag.ROdigerstrasse14. Ordersshouldbeaddressedto: 0-70469Stuttgart,Germany MarstonBookServicesLtd 1'080.269 Allrightsreserved.Thisbook.includingallpartsthereof.isIe· Abingdon.OxonOX144YN gaily protected by copyright. Any use, exploitation.or com Tel: 01235465500 mercialization outside the narrow limits set by copyright Fax: 01235465555 legjslition,withoutthepublishersconsent.isillegalandliable to prosecution.Thisapplies in particularto photostatorme DistributedintheUSAby: chanical reproduction, copying, or duplication of any kind. BlackwellScience,Inc. translating,preparationofmicrofilms,andelectronicdatapro CommercePlace cmingandstorage. 350MilinStreet Malden.MA021485018 Tel: 8007596102 TherightoftheAuthorstobeidentifiedastheAuthorsofthis 781 3BB8250 WorkhasbeenassertedinaccordancewiththeCopyright,De Fax: 781 3888255 signsandPatentsAct1988. DistributedinAustralasiaby: All rights reserved. Nopartofthis publication mayberepro BlackwellScience(Asia)PtyLtd duced,storedinaretrievalsystem.ortransmitted.inanyform 54UnrversityStreet or by i1ny means. electronic. mechanical, photocopying, re Carlton,Victoria3053 cordingorotherwise.exceptaspermittedbytheUKCopyright. Tel: 393470300 DesignsandPatentsAct1988,withoutthepriorpermissionof Fax: 393475001 thecopyrightowner. Acataloguerecordforthistitleisavaililblefrom theBritishu Firstpublished 1999 brary DistributedintheUnitedKingdom.Europe(outsideGermany. Austria and Switzerland), the Middle East, Africa. the Indian CoverdesignbyRuthHammelehle SutxontinentandAsiaby: BlackwellScienceLtd OsneyMead OxfordOXlOEl ISBN-978-0-632-05357-5 v Preface Microbiology is MoreThan the Biochemistryor Why a new Textbook on the Biology of the Molecular Biology of Microorganisms Prokaryotes1 Bacteria were detected in the 17th century as minute Although many cellular components and universal unicellular organisms that lacked any detectable struc biochemical mechanisms are present in all living ture and occurred almost everywhere. Late in the 19th organisms. the tremendous physiological diversity and century. they were identified as a large group of adaptability of the prokaryotes, together with their organisms with distinct and specific physiological fundamental role in environmental, biotechnological, properties,suchastheabilitytofermentcarbohydrates, and medical research and application. justify their to grow photoautotrophically. and to actas pathogens. separate treatment. Hence, this book is restricted to The microbes were grouped systematically together prokaryotic organisms, i.e., the true bacteria (eubacte with other small and allegedly primitive organisms. in ria) and the archaea (archaebacteria). and their viruses particular unicellular algae. fungi. and protozoa. Today (bacteriophages), which at the DNA- or RNA-level we distinguish between prokaryotic and eukaryotic correspond to plasmids and not to trueorganisms. microorganisms. In contrast to eukaryotic cells. pro Molecular biology has developed largely through karyotes lack a nuclear membrane (i.e.. a nucleus). studieswith bacteria.This includes the riseofrecombi mitochondriaand plastids,and mitosisand meiosis. but nant DNAorgene technology. It is safe to concludethat theycontainparticularcellwalland membranecompo despite a shift ofinterest in recent times to eukaryotic nents not found in eukaryotes. Prokaryotes are small, organisms. the prokaryotes will continue to retain a but neither simple nor primitive.At the morphological central place both in fundamental and in applied level. they are not "bags full ofenzymes," but highly biological research. This will, however. require new structured cells, able to grow and multiply at an textbooks, such as this one. which presents an inte astonishing speed. with cell divisions as accurate as in gratedviewoftheprokaryoticcellasanorganismandof the eukaryotes, and with compartments that separate all prokaryotes as a large population in which all various metabolic activities. At the physiological level. organisms communicate among themselves and with however. the immense diversityofthe prokaryotes has the restofthe environment. alwaysbeenconsideredastheirhallmark,togetherwith Bacteria, although autonomous cells and complete theirsurprisingadaptability to environmental changes. organisms. cannot be fully understood if viewed as Biology has been subdivided traditionally. accord single cells. much as a sequenced gene cannot be ingtothemaintypesoforganisms.intobotany.zoology, understood unless itsrole in the biologyofitsorganism and microbiology. The latter dealt with bacteria (pro is also considered. In this context, one of the most karyotes). with eukaryotes of lower complexity, and outstanding capacities of the prokaryotes is their with viruses. Modern biology, however, is subdivided extended horizontal gene transfer under natural condi intosections moredefined bystructuresandorganisms tions. Abacterium has access to any useful gene ofany ofincreasing complexity, in particularfrom macromol other strain and the sum of all the genes of all ecules and genes to the living cells. organisms, and organismsofacommunityconstitutesalargecollective populations. This classification facilitates the recogni genome. Gene transfer, however, is optional and tion of universal principles common to all living involvesonlyasmallpercentageofthegenesinasingle systems. In unicellularorganisms. the cell is by defini transferevent. Ofthese,onlythespecies-specific genes tion also the organism. Their biology thus includes will recombine into the cellular chromosome ofa cell. everythingfromthe molecularstructuresofthecelland All others will be lost by curing unless under counter fromcellularphysiologytodifferentiationprocessesand selection. life in temporary ecosystems of mixed their behavioras membersofcomplexecosystems. populations with complementary metabolic and mor- vi Preface phological capacIties is the prokaryotic equivalent of are suspected to exist or have been analyzed in multicellular life. AIry bacterium with its cellular molecular deta.i1 and wherever new phenomena have chromosome and variable autonomous genetic ele been reported in other bacteria, e.g., sporulation and ments which is a member of an ecosystem thus antibiotic biosynthesis. these have been used as exam resembles a differentiated cell in an eukaryotic multi ples. Moreover, it has been forgotten all too often that cellular organism. Furthermore. because no strict basic research in microbiology is the foundation on geneticisolationexists.speciation is notas pronounced which applied microbiology rests. Most techniques intheprokaryoticworldas intheeukaryoticworld.This dealing with or using prokaryotes in modem medicine, requires a newtypeofsystematics. Viewed in this way. agriculture. industrial production. and en-vironmenta.1 the lifestyle of the archaea (archaebacteria) resembles. processes profited vastly from progress in basic re despite important biochemical differences. the lifestyle search. Wherever new developments and promising ofthe bacteria(eubacteria) more than it resembles that areas in applied microbiology can beantic-ipated. they ofthe eukaryotes. have been pointedout. Pedagogical Aids How Is the Book Organized? Each section is preceded by a general introduction in This book is based on a physiological and functional which the subjects treated and the connections which approachinwhichthediversityoftheprokaryoticworld linkthemarebrieflydescribed.Where possible,linksto is madevisiblebycharacteristicexamplesand inwhich other sections are also indicated. This is especially up.:.and-comingdevelopmentsareindicated.Thebookis conspicuous for Table 20.1, in which major global divided into nine sections; the beginning sections regulatory networks of prokaryotes are listed. These provide the basic facts needed to understand the later networks can best be used, as has been attempted in sections. In this way, the book proceeds from the this book, to define the inherent logic of bacterial description of cellular structures through metabolic metabolism and to bring together seemingly unrelated pathways and metabolic reactions to the genes and phenomena that are parts ofthe same global network. regulatory mechanisms.At a higherlevel ofcomplexity, e.g., bacterial taxes and carbon catabolite control. both cell differentiation processes will be followed by a involved in the quest for food; sporulation and anti description ofthe diversity ofprokaryotes and oftheir bioticbiosynthesis,bothpartofthesamedifferentiation role in the biosphere.The book will end with asection process; and cell surface and chromosomal rearrange on man and microbes, i.e., applied microbiology. ments, both part of pathogen strategies in host infec tion. In all chapters, essential definitions are given and essential conclusions are highlighted in shaded ~as. What Are the Aims and Scope of the Book? Thecorresponding pagesare listed in the Index,and the sum constitutes a glossary. Historical and outstanding The book is written for upper-level undergraduates, experiments,basicand newmethods,orinformationfor graduateand postgraduatestudentsand for researchers the"specialist" appearinboxes.Allofthechaptersoffer working in fundamental research orusing bacteriaonly Further Reading in which mostly recent papers and as .a tool. forex.ample, in recombinant DNAtechnology, reviews are listed that can be used for further studies inbiotechnology,and in medicine. Rather than present and research. Writing, editing.and coordination of the ingallthedetailsknowninbiochemistryandingenetics work was done by a team of individuals, each with and thatcan befound insuchcorrespondingtextbooks, expertise in the area that they covered. A list of their this book concentrates on central concepts of the names and their contribution is given below. We hope thatthegeneral conceptofthe bookanditscontentwill bacterial lifestyle and on the physiological significance thatthevariouscellularstructures.metabolicpathways, increase the fascination of a broad readership for the and regulatory networt<s have. Parts of the book. world ofthe prokaryotes. especially those dealing with the genetics of the prokaryotesand gene control. mayappear"colicentric." This is because much more is understood at all levels Acknowledgements about Escherichia coli than about any other bacterium. even after the complete sequenc-iog of several other Wewould liketoexpressourgratitude toall thosewho bacterial chromosomes. Wherever similar phenomena madethisbookpossible. MrsM.Hauff-Tischendorffrorn Preface vii Georg Thieme Verlag deserves the credit for having figures into a printed book. This is especially true for persuaded us to undertake the writingofa new typeof ourcopyeditors Karen A. Bruneand Lynn Rogers-Blaut. textbook, the type of which she left open to us. We are indebted to the professionals who by some magic transformed our manuscripts and hand-drawn TheEditors ix Addresses SankarAdhya Barbel Friedrich KlausJann LaboratoryofMolecularBiology Humboldt-Universitat Barbarajann NationalCancerInstitute Mathemat.-Naturwissensch. FakultatI Max-Planck-lnstitut fUr Bethesda. Maryland 20892 InstitutfUr BiologiejMikrobiologie Immunbiologie USA ChausseestraBe 117 Stilbeweg 51 10115 Berlin 79108 Freiburg Carl-AlfredAlpert Germany Germany INRA Institut National de la Recherche Agronomique Georg Fuchs DOrries Kemper LaboratoireVivande Albert-Ludwigs-Universitat Institut fUr GenetikderUniversitat zu 78352jouy-en-josas Cedex InstJ.Biologie II - Mikrobiologie Koln France Schanzlestr.1 ZlilpicherStr. 47 79104 Freiburg 50674Koln Germany Germany Ian R. Booth UniversityofAberdeen Dept.ofMolecular+Cell Biology FergalO'Gara RolfKnippers Marishall College DeptofFoodMicrobiology Fakultatflir Biologie UniversityCollegeCork Aberdeen AB9 1AS UniversitatKonstanz Great Britain Cork UniversitatsstraBe 10 Ireland 78464 Konstanz Germany Wolfgang Buckel MikeGoodfellow Fachbereich Biologie DepartmentofMicrobiology UniversitatMarburg Werner Kohler TheMedicalSchool Karl-von-Frisch-Stra&e AdolfReichweinStr. 26 Framlington Place 35043 Marburg 07745jena Newcastle uponTyne NE2 4HH, Germany Germany Great Britain Arnold L Demain Reinhard Kramer jorgHacker DepartmentofBiology lnstitilt fUr Biochemie InstitutfUr Molekulare Massachusetts InstituteofTechnology Infektionsbiologie derUniversitat Kotn 77 MassachusettsAvenue ZillpicherStr.47 Rontgenring 11 Cambridge. Mass.02139 97070Wilrzburg 50674 Koln USA Germany Germany D. N. Dowling WolfgangHillen Achim Kroger Dept.ofFood Microbiology InstitutfUr Mikrobiologie lnstitutfUr Mikrobiologie UniversityCollegeCork und BiochemiederUniversitat Biozentrum Niederursel Cork StaudtstraBe 5 Marie-Curie-Str. 9 Ireland 91058 Erlangen 60439 Frankfurta.M. Germany Germany Gerhart Drews Albert-ludwigs Universitat Gary R.jacobson j.Gijs Kuenen Institut flir BiologieII Boston University LaboratoryofMicrobiology Mikrobiologie DepartmentofBiology DelftUniversityofTechnology SchanzlestraBe 1 2,CummingtonStreet Julianalaan 67A 79104 FreiburgjBr Boston, Mass.02215 2628 BC Delft Germany USA The Netherlands x Addresses Giancarlo Lancini WalterMesser HermannSahm ruc Lepetit Research Center MPl MolekulareGenetik Institut filr Biotechnologie I Via R. Lepetit34 AbteilungTrautner ForschungszenrrumJUlich GmbH 21040Cerrnzano(Varese) Ihnestra8e 73 Postfach 1913 Italy 14195 Berlin 52428Jiilich Germany Germany Erich Lanka KurtNordstrom Bernhard Schink MPI flir MolekulareGenetik DepartmentofMicrobiology FakultatfUr Biologie IhnestraSe'73 Uppsala University Universitat Konstanz 14195Berlin BiomedicalCenter Universitatsstra8e 10 Germany Box581 78464 Konstan2 75123 Uppsala Germany Sweden JosephW. Lengeler Hans-GunterSchlegel F8 Biologie/Chemie UniversitatOsnabrOck M.P. Nuti Institutfur Mikrobiologie Dip\. di BiotechnologieAgrarie UniversitarCotlingen Postfach 4469 49076Osnabrock Universita di Padova CrisebarnstraSe8 Via Gradenigo6 37077Cottingen Germany Padova Germany It~ly Edmondc.c. Un ErkoSt.1ckebrandr Harvard MedicalSchool WernerPansegrau DSM- Deutsche5ammlungvon Dept. of Microbiology and Molecular Institutefor Molecular PlantSciences Mikroorganismen u. Genetics Clusius Laboratory Zellkulturen longwood Avenue Leiden University MascheroderWeg 1b Boston.Mass. 02115 2333 Atu,iden 38124Braunschweig USA The Netherlands Germany PieterW. Postma BrianTindall Wolfgang Ludwig Universiteit vanAmsterdam DSM-Deutschesammlungvon Lehrstuhl file Mikrobiologie E.e. Slater Institute for Biochemical Mikroorganismen u. zellkulruren Technische Universitat MOnchen Research MascheroderWeg1b Arcisstrase21 Plantage Muidergracht 12 38124Braunschweig 802890MOnchen tOl8TVAmsterdam Germany Germany The Netherlands Gottfried Unden Mohamed A. Marahiel UrsulaB. Priefer Institut fUr Mikrobiologie u. Wein UniversitatMarburg Institut fUr Botanik forschung FachbereichChemie Rheinisch-WestfalischeTechnische FB21/Biologie Hans-Meerwein-Stra~ Hochschule Joh. Gutenberg-Univ. Mainz 35043 MarburgjLahn WorringerWeg Becherweg 15 Germany 52056Aachen 5S099Mainz Gennany Germany Frank Mayer Alfred POhler PeterZuber Institut rue Mikrobiologie FakultitfOr BiologieVI (Genetik) Departmentof Biochemistryand Mo Georg-August-UniversitAt Universitat Bielefeld lecular Biology Grisebachstrage8 Postfach 1001 31 louisianaState University 37077 GOttingen 33615 Bielefeld Shreveport.Louisiana Germany Germany USA xi Contents 1 Bacteriology Paved the Way to Cell Biology: a Historical Account ...................... 1 H.G. Schlegel. W. Kohler 1.1 NewConceptsand Experimental 1.10 TheAnalysis ofAnabolicand Catabolic Approaches PavedtheWayfor Progress.... 1 Metabolism lead to the Discoveryof 1.2 ObservationsandSpeculation lead tothe Substrates. Products.Apoenzymes,and FirstConceptofthe ExistenceofLiving Coenzymes,and. in theend.ofMetabolic Infectious Agents......................... 2 Pathways................................. 9 1.3 Bacteriaare Membersofa New, large 1.11 Studies on Inclusion Bodies and the GroupofIndependentOrganisms.......... 3 Structures and Functions ofCell Envelopes 1.4 TheIntroductionofSolid. Defined Media Revealed the Organizationofthe Bacterial and Pure-Culture Methods MarksaTrue Cell...................................... 10 Revolution............................... 4 1.12 BacterialAdaptationwas Well Recognized 1.5 The New Bacteriological Methods Proved Beforethe Genetic Approach Revealed the that the CausativeAgentsofInfectious Basis ofMolecularMechanisms of Diseases are Bacteria ..................... 5 Regulation................................ 11 1.6 Studieson Fermentation Founded Bacterial 1.13 Studiesonthe MetabolicTypesofBacteria Physiologyand Biochemistry.............. 6 Revealed TheirFunctions in the............ 1.7 LithoautotrophyIs theAbilityofBacteriato Biosphere ................................ 12 Obtain Energyfrom the Oxidationof 1.14 TheGoalsand Methodsofthe Classification InorganicCompounds and Carbon from ofBacteria HaveChanged.................. 13 Carbon Dioxide........................... 6 1.15 BacterialViruses(Bacteriophages)Were 1.8 light-DependentProcesses suchas Detectedas lytic Principles................ 13 Phototaxis. light-Induced Energy 1.16 Studieson Heredity in Bacteria Provides the Transduction, and the Photoassimilationof DecisivePrinciplesand Concepts for the Carbon DioxideTooka longTimeto be PromotionofModem Biology Including Understood .............................. 7 GeneTechnology.......................... 14 1.9 Dinitrogen Fixation Is Unique tothe 1.17 Epilogue.................................. 15 Prokaryotes.............................. 8 Section I The Prokaryotic Cell F. Mayer 2 Cellular and Subcellular Organization of Prokaryotes..................................... 20 F. Mayer 2.1 Prokaryotes,Though Small,Containall 2.3 Prokaryotes MayOccuras SingleCellsoras Structural Elements Necessary forSurvival Cen Associations.......................... 25 and Multiplication........................ 20 2.4 TheStructuralComponentsofProkaryotic 2.2 CellularStructuresCan Be MadeVisibleor Cell EnvelopesAre Organized as Barriers and Identified by Numerous Methods.......... 22 Interfaces................................. 27 xII Contents 2.5 The setupofthe IntracellularStructures 2.6 Cell AppendagesServefor Locomotion and Reflectsthe High DegreeofOrganization in Cell Recognition.......................... 41 the ProkaryoticCell ...........••......... 36 1 2.7 Bacteria May FormSporesand Other RestingCells _._ 44 Section II Basic Prerequisites for Cellular Life A Kroger. G. Fuchs 3 Substrate-Level Phosphorylation .............. ............................. 48 A. Kroger 3.1 ATPSynthesis Is Coupled to Exergonic 3.4 A"High·Energy" Compound Is Formed in Reactions................................ 48 SLP..••••••.••...................•....... 52 3.2 TheAllJYield Is a Functionofthe Free 3.5 PyruvateOxidation Is Coupled to Energy Energyofthe Driving Reaction............ 49 Conservation ............................. 55 3.3 CouplingofATPSynthesis toGlucose 3.6 The CatabolicFunctionofthe CitfilteCycle Degradation Requires C-COeavageand Is to Provide Reducing Equivalentsfor SubsequentOxidation .................... 51 Oxidative Phosphorylation................. 55 4 Eledron-Transport-Coupled Phosphorylation.............................................. 59 A KrOger 4.1 In ETP. theAmountofATIJ Formed 4.4 ThereAre Many Different Mechanisms of Corresponds With the Free Energyofthe Coupling ElectronTfilnsport to Proton Driving Redox Reaction................... 59 Transport................................. 65 4.2 All ATIJSynthasesOperateAccordingtothe 4.5 In Photophosphorylation. ElectronTransport SameMechanism........................ 62 and ProtonTranslocation Are Driven by 4.3 ThereAre Many DifferentResp;ratOly Ught..................................... 67 Chains................................... 63 5 Multiple Roles of Prokaryotic Cell Membranes 68 R. Kromer 5.1 BacterialMembranes Functionas 5.5 EnergeticsofCarrier-mediatedTransport: PermeabilityBarriers..................... 68 TheConceptofCoupling................... 73 5.2 TIleStructureand FunctionofTransport Is 5.6 ThereAre Many DifferentTransport Dictated by the Membrane................ 69 Mech.1nisms in Prokaryotes................ 74 5.3 FormalConceptsofTransporterFunction... 70 5.7 Regulation and DiversityofTransport 5.4 Studying Kinetics ofTransport Is Useful for Systems.................................. 84 Identificationand Characterizationof 5.8 secretionofMacromolecules............... 86 Transport Processes ...................... 72 6 Growth and Nutrition......................................................................... 88 G. Fuchs. A. Kroger 6.1 Growth Characteristicsofa BatchCulture 63 Growth Media Provideall Essential Is a Reflection ofCell Physiology........... 88 Nutrients 95 6.2 Physicochemical Factors AffectGrowth and 6.4 SterilizationofM~iaand EquipmentAre a More............................ .... 90 Mustfor Maintaining PureCultures , 99
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