Table Of ContentProkaryotic Metabolism and Physiology
Determination of the genome sequences for a the National University of Malaysia. He has been
wide range of bacteria and archaea has made an honouredbytheKoreanGovernment,whichdesig-
in-depth knowledge of prokaryotic metabolic nated his research group a National Research
functionevenmoreessential inordertogivebio- Laboratory, the Bioelectricity Laboratory, and has
chemical,physiologicalandecologicalmeaningto served as President of the Korean Society for
the genomic information. Clearly describing the Microbiology and Biotechnology. Professor Kim
important metabolic processes that occur under wrote the classic Korean microbiology text on
different conditions and in different environ- MicrobialPhysiologyandhaspublishedover200refer-
ments,thisadvancedtextprovidesanoverviewof eed papers and reviews, and holds over 20 patents
the key cellular processes that determine prokar- relating to applications of his research in environ-
yoticrolesintheenvironment,biotechnologyand mentalandmicrobialbiotechnology.
human health. Structure and composition are
ProfessorGeoffreyMichaelGaddisanauthorityon
describedaswellasthemeansbywhichnutrients
microbial interactions with metals and minerals,
are transported into cells across membranes.
theirgeomicrobialsignificanceandapplicationsin
Discussionofbiosynthesisandgrowthisfollowed
environmental biotechnology. He holds the Boyd
by detailed accounts of glucose metabolism
BaxterChairofBiologyandleadstheGeomicrobio-
through glycolysis, the TCA cycle, electron trans-
logy Group at the University of Dundee and was
port and oxidative phosphorylation, as well as
founding Head of the Division of Molecular
other trophic variations found in prokaryotes
MicrobiologyintheSchoolofLifeSciences.Hehas
including the use of organic compounds other
published over 300 refereed scientific papers,
than glucose, anaerobic fermentation, anaerobic
books,chaptersandreviewsandhasreceivedinvi-
respiration, chemolithotrophy and photosynth-
tationstospeakatinternationalconferencesinover
esis.Theregulationofmetabolismthroughcontrol
30countries.ProfessorGaddhasservedasPresident
ofgeneexpressionandenzymeactivityisalsocov-
oftheBritishMycologicalSocietyandisanelected
ered, as well as the survival mechanisms used
FellowoftheRoyalSocietyofBiology,theAmerican
understarvationconditions.
AcademyofMicrobiology,theLinneanSociety,the
Learned Society of Wales, the Royal Society of
ProfessorByungHongKimisanexpertonanaerobic
Edinburgh and elected Member of the European
metabolism, organic degradation and bioelectro-
Academy of Microbiology. He has received the
chemistry.HegraduatedfromKyungpookNational
Berkeley Prize and President’s Award from the
University, Korea and obtained a PhD from
British Mycological Society, the Charles Thom
University College Cardiff. He has carried out
Award from the Society for Industrial
research at several universities around the world,
Microbiology and the Colworth Prize from the
withanestablishedcareerintheKoreaInstituteof
MicrobiologySocietyforhisresearchcontributions
ScienceandTechnology.Currentlyheisteachingat
tothemicrobiologicalsciences.
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Prokaryotic Metabolism and
Physiology
SECOND EDITION
Byung Hong Kim
KoreaInstituteofScienceandTechnology
NationalUniversityofMalaysia
Geoffrey Michael Gadd
UniversityofDundee
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DOI:10.1017/9781316761625
©ByungHongKimandGeoffreyMichaelGadd2008,2019
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Firstpublished2008
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Contents in brief
1 Introductiontoprokaryoticmetabolismandphysiology page1
2 Compositionandstructureofprokaryoticcells 5
3 Membranetransport–nutrientuptakeandprotein
excretion 31
4 Glycolysis 58
5 Tricarboxylicacid(TCA)cycle,electrontransportand
oxidativephosphorylation 80
6 Biosynthesisandgrowth 115
7 Heterotrophicmetabolismonsubstratesotherthan
glucose 185
8 Anaerobicfermentation 230
9 Anaerobicrespiration 268
10 Chemolithotrophy 321
11 Photosynthesis 351
12 Metabolicregulation 372
13 Energy,environmentandmicrobialsurvival 446
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Contents
Preface pagexxiii
Chapter1 Introductiontoprokaryoticmetabolismand
physiology 1
Furtherreading 3
Chapter2 Compositionandstructureofprokaryoticcells 5
2.1 Elementalcomposition 5
2.2 Importanceofchemicalform 6
2.2.1 Fivemajorelements 6
2.2.2 Oxygen 7
2.2.3 Growthfactors 8
2.3 Structureofmicrobialcells 8
2.3.1 Flagellaandpili 8
2.3.2 Capsulesandslimelayers 10
2.3.3 S-layer,outermembraneandcellwall 11
2.3.3.1 S-layer 11
2.3.3.2 Outermembrane 11
2.3.3.3 Cellwallandperiplasm 15
2.3.4 Cytoplasmicmembrane 19
2.3.4.1 Propertiesandfunctions 19
2.3.4.2 Membranestructure 20
2.3.4.3 Phospholipids 20
2.3.4.4 Proteins 24
2.3.5 Cytoplasm 24
2.3.6 Restingcells 27
Furtherreading 27
Chapter3 Membranetransport–nutrientuptakeand
proteinexcretion 31
3.1 Ionophores:modelsofcarrierproteins 31
3.2 Diffusion 31
3.3 Activetransportandroleofelectrochemicalgradients 32
3.4 ATP-dependenttransport:theATP-bindingcassette(ABC)
pathway 34
3.5 Grouptranslocation 35
3.6 Precursor/productantiport 36
3.7 Ferricion(Fe(III))uptake 37
3.8 TonB-dependentactivetransportacrosstheouter
membraneinGram-negativebacteria 37
3.9 Multidrugeffluxpump 37
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x CONTENTS
3.10 Exportofcellsurfacestructuralcomponents 39
3.10.1 Proteintransport 40
3.10.1.1 Generalsecretorypathway(GSP) 40
3.10.1.2 Twin-argininetranslocation(TAT)pathway 40
3.10.1.3 ATP-bindingcassette(ABC)pathway 42
3.10.1.4 Proteintranslocationthroughthecellwallin
Gram-positivebacteria 43
3.10.2 Proteintranslocationacrosstheoutermembranein
Gram-negativebacteria 43
3.10.2.1 Chaperone/ushersystem 44
3.10.2.2 TypeIsecretionsystem(T1SS):ATP-bindingcassette
(ABC)pathway 45
3.10.2.3 TypeIIsecretionsystem(T2SS) 45
3.10.2.4 TypeIIIsecretionsystem(T3SS) 46
3.10.2.5 TypeIVsecretionsystem(T4SS) 47
3.10.2.6 TypeVsecretionsystem(T5SS):autotransporter
andproteinsrequiringsingleaccessoryfactors 48
3.10.2.7 TypeVIsecretionsystem(T6SS) 49
3.10.2.8 TypeVIIsecretionsystem(T7SS) 50
3.10.2.9 TypeVIIIsecretion(curlibiogenesis)system(T8SS) 51
3.10.3 Exportofpolysaccharides 51
3.10.4 Proteinsecretioninarchaea 53
3.11 Metallochaperones 53
Furtherreading 54
Chapter4 Glycolysis 58
4.1 EMPpathway 59
4.1.1 Phosphofructokinase(PFK):keyenzymeoftheEMPpathway 61
4.1.2 ATPsynthesisandproductionofpyruvate 61
4.1.3 ModifiedEMPpathwaysinbacteria 61
4.1.3.1 Useofatypicalcofactors 61
4.1.3.2 Methylglyoxalbypass 62
4.1.4 ModifiedEMPpathwaysinarchaea 63
4.1.5 RegulationoftheEMPpathway 64
4.1.5.1 Regulationofphosphofructokinase 64
4.1.5.2 Regulationofpyruvatekinase 65
4.1.5.3 RegulationofmodifiedEMPpathwaysinarchaea 65
4.1.5.4 Globalregulation 65
4.2 Glucose-6-phosphatesynthesis:gluconeogenesis 65
4.2.1 PEPsynthesis 65
4.2.2 Fructosediphosphatase 66
4.2.3 Gluconeogenesisinarchaea 66
4.2.4 Regulationofgluconeogenesis 67
4.3 Hexosemonophosphate(HMP)pathway 67
4.3.1 HMPpathwayinthreesteps 67
4.3.2 AdditionalfunctionsoftheHMPpathway 68
4.3.2.1 Utilizationofpentoses 69
4.3.2.2 OxidativeHMPcycle 69
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CONTENTS xi
4.3.3 RegulationoftheHMPpathway 69
4.3.4 F -dependentglucose-6-phosphatedehydrogenase 69
420
4.3.5 HMPpathwayandarchaea 70
4.4 Entner–Doudoroff(ED)pathway 70
4.4.1 GlycolyticpathwayinsomeGram-negativebacteria 70
4.4.2 KeyenzymesoftheEDpathway 71
4.4.3 ModifiedEDpathways 72
4.4.3.1 ExtracellularoxidationofglucosebyGram-negative
bacteria 72
4.4.3.2 ModifiedEDpathwaysinarchaea 73
4.5 Phosphoketolasepathways 73
4.5.1 GlucosefermentationbyLeuconostocmesenteroides 73
4.5.2 Bifidumpathway 75
4.6 Glycolysisinarchaea 75
4.7 Useofradiorespirometrytodetermineglycolyticpathways 76
Furtherreading 77
Chapter5 Tricarboxylicacid(TCA)cycle,electrontransport
andoxidativephosphorylation 80
5.1 Oxidativedecarboxylationofpyruvate 80
5.2 Tricarboxylicacid(TCA)cycle 81
5.2.1 CitratesynthesisandtheTCAcycle 81
5.2.2 ModifiedTCAcycle 82
5.2.3 RegulationoftheTCAcycle 83
5.3 ReplenishmentofTCAcycleintermediates 83
5.3.1 Anapleroticsequence 84
5.3.2 Glyoxylatecycle 84
5.3.2.1 Regulationoftheglyoxylatecycle 85
5.3.3 Ethylmalonyl-CoApathway 85
5.3.4 Methylaspartatecycle 86
5.4 IncompleteTCAforkandreductiveTCAcycle 86
5.4.1 IncompleteTCAfork 87
5.4.2 ReductiveTCAcycle 87
5.5 Energytransductioninprokaryotes 88
5.5.1 Freeenergy 89
5.5.1.1 ΔG00fromthefreeenergyofformation 89
5.5.1.2 ΔG00fromtheequilibriumconstant 90
5.5.1.3 ΔGfromΔG00 90
5.5.1.4 ΔG00fromΔG0 90
5.5.2 Freeenergyofanoxidation/reductionreaction 91
5.5.2.1 Oxidation/reductionpotential 91
5.5.2.2 FreeenergyfromΔE00 91
5.5.3 Freeenergyofosmoticpressure 92
5.5.4 Sumoffreeenergychangeinaseriesofreactions 93
5.6 RoleofATPinthebiologicalenergytransductionprocess 93
5.6.1 Highenergyphosphatebonds 94
5.6.2 Adenylateenergycharge 94
5.6.3 Phosphorylationpotential(ΔGp) 95
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xii CONTENTS
5.6.4 InterconversionofATPandtheprotonmotiveforce(Δp) 96
5.6.5 Substrate-levelphosphorylation(SLP) 96
5.7 Protonmotiveforce(Δp) 96
5.7.1 Protongradientandmembranepotential 96
5.7.2 Acidophilesandalkaliphiles 96
5.7.3 Protonmotiveforceinacidophiles 97
5.7.4 Protonmotiveforceandsodiummotiveforceinalkaliphiles 98
5.8 Electrontransport(oxidative)phosphorylation 98
5.8.1 Chemiosmotictheory 98
5.8.2 Electroncarriersandtheelectrontransportchain 99
5.8.2.1 Mitochondrialelectrontransportchain 99
5.8.2.2 Electroncarriers 100
5.8.2.3 Diversityofelectrontransportchainsinprokaryotes 101
5.8.2.4 Inhibitorsofelectrontransportphosphorylation(ETP) 104
5.8.2.5 Transhydrogenase 104
5.8.3 ArrangementofelectroncarriersintheH+-translocating
membrane 104
5.8.3.1 Q-cycleandQ-loop 105
5.8.3.2 Protonpump 105
5.8.3.3 Sodiumpump 106
5.8.4 ATPsynthesis 107
5.8.4.1 ATPsynthase 107
5.8.4.2 H+/Oratio 107
5.8.4.3 H+/ATPstoichiometry 108
5.8.5 Uncouplers 108
5.8.6 PrimaryH+(Na+)pumpsinfermentativemetabolism 109
5.8.6.1 Fumaratereductase 109
5.8.6.2 Na+-dependentdecarboxylase 109
5.8.6.3 Δpformationthroughfermentationproduct/H+
symport 110
5.8.6.4 Energyconservationthroughelectronbifurcation 110
5.8.6.5 Energy-convertinghydrogenase 110
5.8.6.6 H+(Na+)-translocatingferredoxin:NAD+
oxidoreductase 110
5.9 Otherbiologicalenergytransductionprocesses 111
5.9.1 Bacterialbioluminescence 111
5.9.2 Electricityasanenergysource 111
Furtherreading 112
Chapter6 Biosynthesisandgrowth 115
6.1 Molecularcompositionofbacterialcells 115
6.2 Assimilationofinorganicnitrogen 115
6.2.1 Nitrogenfixation 116
6.2.1.1 N -fixingorganisms 116
2
6.2.1.2 BiochemistryofN fixation 117
2
6.2.1.3 BioenergeticsofN fixation 120
2
6.2.1.4 MolecularoxygenandN fixation 120
2
6.2.1.5 RegulationofN fixation 122
2
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