Biology of the Prokaryotes

975 Pages·1998·176.15 MB·English

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: [phone]
mercialization outside the narrow limits set by copyright Fax: [phone]
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: [phone]
TherightoftheAuthorstobeidentifiedastheAuthorsofthis 781 3BB8250
WorkhasbeenassertedinaccordancewiththeCopyright,De Fax: [phone]
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: [phone]
DesignsandPatentsAct1988,withoutthepriorpermissionof Fax: [phone]
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