Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and ...

87 Pages·2014·11.34 MB·English

Carbohydrate Metabolism in Archaea: Current Insights into Unusual
Enzymes and Pathways and Their Regulation
ChristopherBräsen,DominikEsser,BernadetteRauch,BettinaSiebers
MolecularEnzymeTechnologyandBiochemistry,BiofilmCentre,FacultyofChemistry,UniversityofDuisburg-Essen,Essen,Germany
SUMMARY...................................................................................................................................................91
INTRODUCTION..............................................................................................................................................91
MODIFICATIONSOFTHEEMBDEN-MEYERHOF-PARNASPATHWAYINARCHAEA.........................................................................92
GlucosePhosphorylation..................................................................................................................................94
ADP-dependentglucokinase...........................................................................................................................94
D
ROKhexokinase.........................................................................................................................................95
o
Otherarchaealsugarkinases............................................................................................................................95
w
PhosphoglucoseIsomerase................................................................................................................................98 n
Phosphoglucoseisomerase/phosphomannoseisomerase..............................................................................................98 lo
Cupin-typephosphoglucoseisomerase...............................................................................................................100 a
Phosphofructokinase.....................................................................................................................................100 d
e
Pyrophosphate-dependentphosphofructokinase.....................................................................................................100 d
ADP-dependentphosphofructokinase................................................................................................................100
f
ATP-dependentphosphofructokinase(PFK-B).........................................................................................................101 ro
Fructose-1,6-BisphosphateAldolase(Catabolic)..........................................................................................................101 m
TriosephosphateIsomerase..............................................................................................................................102
h
Glyceraldehyde3-PhosphateOxidation..................................................................................................................103 t
t
Glyceraldehyde-3-phosphate:ferredoxinoxidoreductase.............................................................................................104 p
Nonphosphorylatingglyceraldehyde-3-phosphatedehydrogenase..................................................................................104 :/
/
Glyceraldehyde-3-phosphatedehydrogenase(phosphorylating)(catabolic).........................................................................105 m
PhosphoglycerateKinase.................................................................................................................................106 m
PhosphoglycerateMutase................................................................................................................................107 b
2,3-Bisphosphoglyceratecofactor-dependentphosphoglyceratemutase............................................................................107 r.
a
Cofactor-independentphosphoglyceratemutase....................................................................................................107 s
Enolase...................................................................................................................................................108 m
PhosphoenolpyruvateConversiontoPyruvate..........................................................................................................108 .
o
Pyruvatekinase........................................................................................................................................108 r
g
MODIFICATIONSOFTHEENTNER-DOUDOROFFPATHWAYINARCHAEA................................................................................109
/
GlucoseDehydrogenase.................................................................................................................................110 o
GluconateDehydratase..................................................................................................................................113 n

2-Keto-3-DeoxygluconateKinase.........................................................................................................................114 M
2-Keto-3-Deoxy-(6-Phospho)GluconateAldolase[KD(P)GA].............................................................................................114 a
GAPConversion..........................................................................................................................................115 rc
Glyceraldehydedehydrogenase/(glycer)aldehyde:ferredoxinoxidoreductase........................................................................115 h
GlycerateKinase..........................................................................................................................................116 2
GLUCONEOGENESIS........................................................................................................................................116 8
,
PhosphoenolpyruvateSynthetase.......................................................................................................................116 2
Pyruvate:PhosphateDikinase.............................................................................................................................117 0
PhosphoenolpyruvateCarboxykinase....................................................................................................................117 1
9
Glyceraldehyde-3-PhosphateDehydrogenase/PhosphoglycerateKinase...............................................................................119
b
BifunctionalFructose-1,6-BisphosphateAldolase/Phosphatase..........................................................................................119
y
PENTOSEDEGRADATIONPATHWAYSINARCHAEA.......................................................................................................120
g
PentoseOxidationandXyloseDehydrogenase/ArabinoseDehydrogenase.............................................................................122 u
C SugarAcidDehydrationandXylonateDehydratase/ArabinonateDehydratase......................................................................125 e
5 s
2-Keto-3-DeoxyxylonateDehydratase/2-Keto-3-DeoxyarabinonateDehydratase.......................................................................126 t
(cid:2)-KetoglutarateSemialdehydeDehydrogenase.........................................................................................................126
2-Keto-3-Deoxyxylonate(KDX)/2-Keto-3-Deoxyarabinonate(KDA)Cleavage............................................................................127
ConversionofGlycolaldehydetoMalate.................................................................................................................127
(continued)
AddresscorrespondencetoChristopherBräsen,[email protected],
orBettinaSiebers,[email protected].
Copyright©2014,AmericanSocietyforMicrobiology.AllRightsReserved.
doi:10.1128/MMBR.00041-13
March2014 Volume78 Number1 MicrobiologyandMolecularBiologyReviews p.89–175 mmbr.asm.org 89
Bräsenetal.
PENTOSESYNTHESISPATHWAYSINARCHAEA............................................................................................................127
HexulosephosphateSynthase/PhosphohexuloseIsomerase.............................................................................................129
Ribose-5-PhosphateIsomerase...........................................................................................................................129
Transketolase.............................................................................................................................................132
AlternativePathwaysforC-C Interconversion..........................................................................................................132
5 3
METABOLICANDREGULATORYCHARACTERISTICSOFWELL-STUDIEDARCHAEALMODELORGANISMS..............................................132
RegulationattheTranscriptLevel........................................................................................................................132
RegulationattheProteinLevel...........................................................................................................................133
MetabolicThermoadaptation............................................................................................................................133
Thermococcales(PyrococcusfuriosusandThermococcuskodakarensis)..................................................................................1.34
Growthconditions.....................................................................................................................................134
Sugartransport........................................................................................................................................134
Sugarmetabolism.....................................................................................................................................135
(i)ThemodifiedEMPpathway......................................................................................................................135
(ii)Gluconeogenesis................................................................................................................................135
D
Energetics..............................................................................................................................................137
o
Regulationattheproteinlevel.........................................................................................................................137
w
Regulationatthegenelevel...........................................................................................................................137 n
TranscriptionalregulatorTrmBinThermococcales.....................................................................................................138 lo
TrmB-likeregulatorsinThermococcales................................................................................................................139 a
(i)TrmB-likeregulatorsinTco.kodakarensis.........................................................................................................139 d
e
(ii)TrmB-likeregulatorsinPyrococcusfuriosus.......................................................................................................140 d
InvivofunctionofTrmBandTrmB-likeregulatorsinPyrococcus.......................................................................................140
f
Sulfolobussolfataricus ....................................................................................................................................140 ro
Growthconditions.....................................................................................................................................140 m
Sugartransport........................................................................................................................................143
h
Sugarmetabolism.....................................................................................................................................143 t
t
(i)ThepromiscuousbranchedEDpathway.........................................................................................................143 p
(ii)SignificanceofbothEDbranches................................................................................................................144 :/
/
(iii)Gluconeogenesis................................................................................................................................144 m
Energetics..............................................................................................................................................144 m
Regulation.............................................................................................................................................144 b
(i)Regulationattheenzymelevelbyallostericeffectors............................................................................................144 r.
a
(ii)Regulationatthetranslationallevel..............................................................................................................145 s
(iii)Regulationattheposttranslationallevelbyproteinphosphorylation...........................................................................145 m
(iv)Regulationatthegene/transcriptlevel.........................................................................................................146 .
o
Transcriptionalregulatorsofthecentralcarbohydratemetabolism...................................................................................146 r
g
Thermoplasmatales(ThermoplasmaacidophilumandPicrophilustorridus) ..............................................................................1.47
/
Growthconditions.....................................................................................................................................147 o
Sugar(glucose)metabolism...........................................................................................................................147 n

Energetics..............................................................................................................................................147 M
Firstinsightsintoregulationattheproteinandgenelevels...........................................................................................147 a
Thermoproteustenax .....................................................................................................................................148 rc
Growthconditions.....................................................................................................................................148 h
Sugartransport........................................................................................................................................148 2
Sugar(glucose)metabolism...........................................................................................................................148 8
,
(i)ThemodifiedEMPpathway......................................................................................................................148 2
(ii)ThebranchedEDpathway.......................................................................................................................150 0
(iii)Gluconeogenesis................................................................................................................................150 1
9
Energetics..............................................................................................................................................150
b
Regulationattheproteinandgenelevels.............................................................................................................150
y
(i)Regulationattheenzymelevelbyallostericeffectors............................................................................................150
g
(ii)Regulationatthegene/transcriptlevel..........................................................................................................151 u
Haloarchaea(Haloferaxvolcanii,Haloarculamarismortui,andHalobacteriumsalinarum) ...............................................................1.52 e
s
Growthconditions.....................................................................................................................................152 t
Sugartransport........................................................................................................................................152
Sugarmetabolism.....................................................................................................................................152
(i)Differentdegradationpathwaysforglucoseandfructose.......................................................................................152
(ii)Glucose-fructosediauxie.........................................................................................................................154
Energetics..............................................................................................................................................154
Regulationatthegeneandproteinlevels.............................................................................................................154
Glycerol-mediatedcataboliterepression..............................................................................................................155
TranscriptionalregulatorGlpR........................................................................................................................1.55
Halobacteriumsalinarum...............................................................................................................................155
(i)TrmB-liketranscriptionalregulator...............................................................................................................155
Methanogens............................................................................................................................................156
(continued)
90 mmbr.asm.org MicrobiologyandMolecularBiologyReviews
UniqueFeaturesofArchaealCarbohydrateMetabolism
Growthconditions.....................................................................................................................................156
Sugar(endogenousglycogen)metabolism...........................................................................................................157
Energetics..............................................................................................................................................157
Regulationatthegeneandproteinlevels.............................................................................................................157
CONCLUSION...............................................................................................................................................159
ACKNOWLEDGMENTS......................................................................................................................................159
REFERENCES................................................................................................................................................159
SUMMARY archaeal membrane lipids composed of isoprenoid chains ether
ThemetabolismofArchaea,thethirddomainoflife,resemblesin linked to sn-glycerol 1-phosphate head groups (i.e., dibiphyta-
itscomplexitythoseofBacteriaandlowerEukarya.However,this nyltetraethers or biphytanylethers) rather than fatty acids ester
metaboliccomplexityinArchaeaisaccompaniedbytheabsenceof linkedtosn-glycerol3-phosphate,asfoundinBacteriaandEu-
D
many “classical” pathways, particularly in central carbohydrate karya(13).Inaddition,murein,thetypicalpeptidoglycanofbac- o
metabolism.Instead,Archaeaarecharacterizedbythepresenceof terialcellwalls,isabsentinArchaea,and,forexample,pseudo- w
unique,modifiedvariantsofclassicalpathwayssuchastheEmb- murein (e.g., Methanosphaera and Methanothermus), S-layer nlo
den-Meyerhof-Parnas(EMP)pathwayandtheEntner-Doudoroff proteins (e.g., Thermoproteus spp. and Sulfolobales), or no cell a
(ED) pathway. The pentose phosphate pathway is only partly envelopes(e.g.,Thermoplasmatales)arefound. d
e
present(ifatall),andpentosedegradationalsosignificantlydiffers Withrespecttotheirlife-styleandmetaboliccomplexity,Ar- d

fromthatknownforbacterialmodelorganisms.Thesemodifica- chaea resemble Bacteria and lower Eukarya, and chemolithoau- fr
o
tions are accompanied by the invention of “new,” unusual en- totrophic, chemoorgangoheterotrophic, as well as phototrophic m
zymeswhichcausefundamentalconsequencesfortheunderlying (aerobic/anaerobic)growthhasbeenreported(14,15).However,
h
regulatoryprinciples,andclassicalallostericregulationsiteswell thismetaboliccomplexityinArchaeaisaccompaniedbytheab- tt
p
establishedinBacteriaandEukaryaarelost.Theaimofthisreview senceofmany“classical”pathwaysknownforBacteriaandEu- :
/
is to present the current understanding of central carbohydrate karya. Instead, Archaea are characterized by the presence of /m
metabolicpathwaysandtheirregulationinArchaea.Inorderto unique pathways, e.g., methanogenesis, and/or by some unusual, m
giveanoverviewoftheircomplexity,pathwaymodificationsare modified-pathwayversionsoftheclassicalroutes.Thisespeciallyap- b
r
discussed with respect to unusual archaeal biocatalysts, their plies to central carbohydrate metabolism (CCM). Only modified .a
structural and mechanistic characteristics, and their regulatory variantsofclassicalsugardegradationpathwayssuchastheEmbden- s
m
propertiesincomparisontotheirclassiccounterpartsfromBac- Meyerhof-Parnas(EMP)pathwayandtheEntner-Doudoroff(ED) .
o
teriaandEukarya.Furthermore,anoverviewfocusingonhexose pathwayhavebeenidentifiedinArchaea.Thepentosephosphate r
g
metabolic,i.e.,glycolyticaswellasgluconeogenic,pathwaysiden- pathway(PPP)ispresentonlypartly(ifatall),andpentosedeg- /

o
tifiedinarchaealmodelorganismsisgiven.Theirenergygainis radationsignificantlydiffersfromthatknownforbacterialmodel n
discussed,andnewinsightsintodifferentlevelsofregulationthat organismssuchasEscherichiacoli.Particularly,themodifications M
have been observed so far, including the transcript and protein anddistinctfeaturesofthesugardegradationpathwayscausefun- a
r
levels(e.g.,generegulation,knowntranscriptionregulators,and damentalconsequencesfortheunderlyingregulatoryprinciples. c
h
posttranslationalmodificationviareversibleproteinphosphory- Notably,thevastmajorityofmetabolicconversionsand,thus,
2
lation),arepresented. intermediates found in the glycolytic and also gluconeogenic 8
,
pathwaysforglucose-to-pyruvateinterconversionareconserved 2
INTRODUCTION inallthreedomainsoflife,highlightinggovernmentbythermo- 0
1
Archaea were established as the third domain of life besides dynamic and chemical constraints (e.g., flux rates/short path- 9

BacteriaandEukaryaonly30yearsago(1,2).Todate,most ways)(16).However,inArchaea,theenzymesinvolvedintheir b
y
cultivable species are adapted to extreme environments, where conversionoftensharenosimilaritywiththeirbacterialandeu- g
theyconstitutethedominantmajority,orharboruniquemetabolic karyoticcounterpartsandrepresentmembersofnewenzymefami- u
e
capabilitieslikemethanogens.Theso-called“extremophiles”thrive lies. Accordingly, by using a comparative genomics approach, the s
inhostilehabitatscharacterizedbyextremesoftemperature,pH,salt, “central core and variable shell” of archaeal genomes were estab- t
or combinations thereof. However, metagenomic/environmental lished,andseveralmissinglinksinarchaealcentralmetabolismwere
molecularbiologyapproachesrevealedthatArchaeaareubiquitous identified,whichareconservedinbacterialandeukaryoticmetabo-
andwidelydistributedinmoderatehabitatsandplayamajorrole lism(17,18).Theseidentified“gaps”inarchaealcentralmetabolic
ingeochemicalcycles(3–5). pathwaysaretheproductofnonhomologousgenereplacement.In
Archaeaexhibitamosaiccharacter,astheysharesometypical themeantime,manyofthesepathwayholeshavebeenclosedbythe
bacterial and eukaryotic properties. Their unicellular life-style, identification of the respective candidates by using comparative
lack of organelles, cell size and shape, as well as DNA structure genomics-basedapproachesand/orclassicalbiochemistry.
(e.g.,onecircularchromosome,operonstructures,andplasmids) Today,267archaealgenomesequenceshavebeencompleted
resemblethoseofBacteria,whereasmostmechanismsinvolvedin (asofDecember2013)(GenomeOnlineDatabase[GOLD][http:
information processing (e.g., replication, transcription, repair, //genomesonline.org/]), and six main archaeal phyla have been
andtranslation)aregenerallyregardedaslesscomplexversionsof proposed: Crenarchaeota, Euryarchaeota, Nanoarchaeota, Thau-
the respective eukaryotic equivalents (6–12). However, Archaea marchaeota, Korarchaeota, and the recently proposed Aigar-
also possess unique archaeal features, most notably the unique chaeota.
March2014 Volume78 Number1 mmbr.asm.org 91
Bräsenetal.
The two largest and first-established phyla are the Euryar- thephysiologicalsignificanceofgenescouldbestudiedbymutant
chaeotaandtheCrenarchaeota(2).TheEuryarchaeotacompriseall construction(forreviewsandliterature,seereferences27and28).
methanogens and extreme halophiles and some thermoacido- Furthermore, transcriptomic (microarray analyses and deep se-
philesand(hyper)thermophiles,whereastheCrenarchaeotacon- quencing in combination with reverse transcription-quantitative
tain only (hyper)thermophilic species (2). The Nanoarchaeota PCR[qRT-PCR]),proteomic,andmetabolomicaswellassystems
compriseonlytwospeciessofar:Nanoarchaeumequitans,which biologyapproacheswerealsousedforArchaea,facilitatingthein-
canbegrownonlyincoculturewiththecrenarchaeoteIgnicoccus vestigationofpathwayregulationandunderlyingprinciples.
hospitalis,andNst1,wherethelikelyhostisamemberoftheSul- Theaimofthisreviewistopresentthecurrentunderstanding
folobales(Acd1)(19,20).TheKorarchaeotainsteadcontainonly ofsugardegradationpathwaysandtheirregulationinArchaea.In
uncultivatedhyperthermophilic,anaerobicArchaea,andthehet- ordertogiveanoverviewofthecomplexity,thisreviewissubdi-
erotrophic organism “Candidatus Korarchaeum cryptofilum” is videdintotwoparts.Thefirstpartfocusesonpathwaymodifica-
thefirstproposedmemberofthisgroup(21,22).Membersofthe tionwithrespecttounusualarchaealbiocatalysts,theirstructural
Thaumarchaeota are both thermophiles and mesophiles and andmechanisticcharacteristics,andtheirregulatorypropertiesin
thrive in very different environmental niches (e.g., freshwater, comparison to their classic counterparts from Bacteria and Eu- D
soil,ocean,andhotsprings)(23,24).Allmembersofthisphylum karya.Inthesecondpart,anoverviewfocusingonhexosemeta- o
w
characterizedsofar(e.g.,Nitrososphaeragargensis,Nitrosopumilus bolicpathways,i.e.,glycolysisaswellasgluconeogenesis,identi-
n
maritimus, and Cenarchaeum symbiosum) are chemolithoau- fied in archaeal model organisms is given. Their energy gain is lo
totrophicammoniaoxidizers,whichwasthoughttobeperformed discussed,andnewinsightsintothedifferentlevelsofregulation a
d
solely by Betaproteobacteria and Gammaproteobacteria (24). thathavebeenobservedsofar,includingthetranscriptandpro- e
d
HWCG1istheonlyidentifiedmemberoftheAigarchaeotasofar teinlevels(e.g.,generegulation,knowntranscriptionregulators,
f
(25). However, whether the Aigarchaeota are indeed a new ar- andposttranslationalmodification[PTM]viareversibleprotein ro
chaealphylumoradeeplybranchingthaumarchaeallineageisstill phosphorylation),arepresented(forpreviousreviewsinthefield m
amatterofdebate(26). of archaeal central carbohydrate metabolism, see references 14 h
t
WhereasthecarbohydratemetabolismofmembersoftheCre- and29–37)(seeFig.1and12forthemostfrequentlyusedabbre- tp
narchaeota and Euryarchaeota has been studied in considerable viationsforenzymesandmetabolicintermediates). :/
/
detail, only little information is available for the remaining ar- m
chaealphyla.InArchaea,sugardegradationwasfirstinvestigated MODIFICATIONSOFTHEEMBDEN-MEYERHOF-PARNAS m
inaerobicextremehalophiles,suchasHalobacteriumsp.andHa- PATHWAYINARCHAEA br
.
loarcula, and thermophilic acidophiles, e.g., the euryarchaeon TheEMPpathwaycanberegardedasanevolutionarilyoptimized a
s
ThermoplasmaacidophilumandthecrenarchaeonSulfolobussol- pathwayfortheconversion/oxidationofglucoseto2moleculesof m
fataricus. In the early 1990s, anaerobic hyperthermophiles, in- pyruvate,yieldingATPaswellasreducingequivalentsandinter- .o
cludingthefermentativelygrowingeuryarchaeonPyrococcusfu- mediatesasprecursorsforcellularbuildingblocks.Pathwayopti- rg
riosus and the crenarchaeon Thermoproteus tenax, growing on mizationmeansthatproductformationisachievedinthefewest /
o
sugarsbymeansofsulfurrespiration,werealsoextensivelyinves- possiblestepswithoverallexergonismtodrivethewholeprocess. n

tigated,andthesestudieshavebeenextendedtootheranaerobic Theaimistoensurethehighestpossibleeffectivity/fluxesonthe M
hyperthermophilessuchasmembersoftheEuryarchaeota(Ther- onehandandtoenablethehighestpossibleenergy/ATPyieldson a
r
mococcusspp.andArchaeoglobusfulgidus)andtheCrenarchaeota theotherhand.Thesepurposesareachievedundertheconsider- c
h
(Desulfurococcus amylolyticus and the [micro]aerophilic/aerobic ationofchemicalandmechanisticfeasibilitiesaswellasthephys- 2
organismsPyrobaculumaerophilumandAeropyrumpernix).Also, icochemicalpropertiesofintermediateswithrespectto,e.g.,sta- 8
,
the most acidophilic organism known to date, the moderately bility,permeability,polarity,andtoxicity(16,38). 2
0
thermophiliceuryarchaeonPicrophilustorridus,hasbeeninvesti- In the classical EMP pathway, glucose is phosphorylated to
1
gated,andtheroleofsugar-metabolizingroutesinsomemetha- glucose6-phosphate(G6P)eitherbyATP-dependenthexokinase 9

nogenic organisms, such as Methanococcus maripaludis and (HK)/glucokinase(GLK)or,inmanyBacteria,bytheactionofthe b
y
Methanocaldococcusjannaschii,havebeenaddressed. phosphoenolpyruvate (PEP) phosphotransferase system (PTS). g
Byusing13Cnuclearmagneticresonance(NMR)analyses,the G6Pisthenisomerizedtofructose6-phosphate(F6P)viaphos- u
e
questionofpathwayutilization,i.e.,whethertheEMPpathway, phoglucoseisomeraseandisagainphosphorylatedtoformfruc- s
t
theEDpathway,orbothroutesareutilizedforsugardegradation tose 1,6-bisphosphate (F1,6BP), a key intermediate of the EMP
in the respective organisms, and to which extent, has been ad- pathway, by phosphofructokinase. F1,6BP is cleaved to dihy-
dressed.Withclassicalbiochemicaltechniqueslikeenzymemea- droxyacetone phosphate (DHAP) and glyceraldehyde 3-phos-
surementsincrudeextracts,nativeproteinpurification,aswellas phate(GAP),catalyzedbyF1,6BPaldolase.DHAPisconvertedto
comparative genome analyses and with molecular biological GAPviatriosephosphateisomerase(TIM),andGAPisoxidizedto
methodslikerecombinantexpressionofcandidateenzymes,the 1,3-bisphosphoglycerate(1,3BPG)throughtheactionofglyceral-
pathways could be reconstructed. The enzymes involved in the dehyde-3-phosphate dehydrogenase (GAPDH), yielding NA-
pathwayshavebeenidentifiedandcharacterized,andthestruc- D(P)H.Thephosphatemoietyfromtheacidanhydride1,3BPGis
turesofmoreandmoreofthearchaealenzymesinvolvedinsugar transferredtoADP,yieldingATPinthefirststepofsubstrate-level
metabolismhavebeendetermined.Also,“genetictoolboxes”fora phosphorylationwithinthepathway,catalyzedbyphosphoglyc-
number of archaeal model organisms, e.g., Haloferax volcanii, erate kinase (PGK). The resulting 3-phosphoglycerate (3PG) is
Thermococcus kodakarensis, Sul. solfataricus, Sulfolobus acidocal- further converted to 2-phosphoglycerate (2PG) and the phos-
darius,andPyr.furiosus,aswellasmethanogenssuchasMetha- phoenolesterPEPviaphosphoglyceratemutase(PGAM)andeno-
nococcusspp.andMethanosarcinaspp.havebeenestablished,and lase(ENO).FromPEP,thephosphatemoietyisagaintransferred
92 mmbr.asm.org MicrobiologyandMolecularBiologyReviews
UniqueFeaturesofArchaealCarbohydrateMetabolism
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FIG1GlucosedegradationviatheEMPpathwayknownformostBacteriaandEukarya(classical)andthemodifiedEMPversionsreportedforArchaea. a
r
Allostericallyregulatedenzymesaredepictedinred.Abbreviations:ENO,enolase;FBPA,fructose-1,6-bisphosphatealdolase;GAPDH,glyceraldehyde-3- c
phosphatedehydrogenase;GAPN,nonphosphorylatingGAPDH;GAPOR,GAP:Fdoxidoreductase;GLK,glucosekinase;HK,hexokinase;PEPS,PEPsynthe- h

tase;PFK,phosphofructokinase;PGI,phosphoglucoseisomerase;PGI/PMI,phosphoglucoseisomerase/phosphomannoseisomerase;cPGI,cupin-typephos- 2
8
phoglucose isomerase; PGAM, phosphoglycerate mutase (dPGAM, 2,3-bisphosphoglycerate [2,3BPG] cofactor dependent; iPGAM, 2,3BPG cofactor
,
independent);PK,pyruvatekinase;PPDK,pyruvate:phosphatedikinase;ROK,hexokinaseoftherepressorprotein,openreadingframe,sugarkinasefamily; 2
G6P,glucose6-phosphate;F6P,fructose6-phosphate;F1,6BP,fructose1,6-bisphosphate;DHAP,dihydroxyacetonephosphate;GAP,glyceraldehyde3-phos- 0
1
phate;1,3BPG,1,3-bisphosphoglycerate;3PG,3-phosphoglycerate;2PG,2-phosphoglycerate;PEP,phosphoenolpyruvate. 9

b
y
toADPviasubstrate-levelphosphorylationtofinallyformpyru- Duetoitscomparativelyhighenergyyieldofmaximally2mol g
vateinthepyruvatekinase(PK)-catalyzedreaction(foranover- ATP/molofglucose,theutilizationoftheEMPpathwayispartic- u
e
view,seeFig.1).Thus,theconversionof2molGAPtopyruvate ularlyadvantageousfororganismswithananaerobicorfaculta- s
t
yields4molATPinthePGKandPKreactions,and2molATPhas tivelyanaerobiclife-stylegainingenergymainlybyfermentative
tobeinvestedforphosphorylationofglucoseandF6Pinthepre- metabolismfromsugars/glucose.Accordingly,byusing13CNMR
paratoryphaseofglycolysis,resultinginanetyieldof2molATP studiesincombinationwithenzymemeasurementsincrudeex-
permolglucoseoxidizedtopyruvate.Withinthispathway,phos- tracts, the anaerobic hyperthermophiles, the Euryarchaeota Pyr.
phorylationfromglucosetoG6PandfromF6PtoF1,6BPaswell furiosusandThermococcusspp.,andthecrenarchaeonDesulfuro-
aspyruvateformationfromPEPrepresentirreversiblesteps,and coccusfermentativelygrowingonsugarshavebeenshowntode-
theenzymesinvolvedareaccordinglythemainpointsofallosteric gradeglucose100%viamodifiedEMPpathways.Also,thecren-
regulation.Also,theseirreversiblereactions,especiallythePKand archaeonTpt.tenax,growingonglucoseusingsulfurreduction,
phosphofructokinase(PFK)reactions,havetobebypassedduring metabolizesthesugar85%viaanEMPpathwaymodification(39,
gluconeogenesis.ThisisusuallyaccomplishedbyPEPsynthetase 40).Fortheanaerobic,euryarchaealsulfatereducerArc.fulgidus
(PEPS), pyruvate:phosphate dikinase (PPDK), or the pyruvate aswellasthemicroaerophilicCrenarchaeotaPyb.aerophilumand
carboxylase/PEPcarboxykinase(PCK)enzymecoupleforthePK Aer.pernix,modifiedEMPversionshavealsobeendescribedon
reactionandfructosebisphosphatase(FBPase)forthePFKreac- thebasisofenzymeanalyses(41,42).Underliningtheoptimized
tion. propertiesoftheEMPpathwayandthethermodynamic,kinetic,
March2014 Volume78 Number1 mmbr.asm.org 93
Bräsenetal.
and mechanistic constraints under which the pathway evolved, archaealEMPpathwayversionsaswellastheclassicalEMPpath-
glucosedegradationviathesemodifiedEMPpathwayversionsin wayfromBacteriaandEukarya).
Archaeabasicallyproceedsviathesameintermediatesknownfor
theclassicalEMPpathwayinBacteriaandEukarya,alsohighlight- GlucosePhosphorylation
ing the ancestral character of the pathway. However, although ThefirststepinthemodifiedEMpathwaysofArchaeaisthephos-
catalyzing the same conversions, the enzymes in archaeal EMP phorylation of glucose to glucose 6-phosphate. In Bacteria, this
pathwayversionsdifferremarkably(seeFig.1foracomparative process is coupled to transport via the PEP phosphotransferase
illustration of the classical EMP pathway and the modified ar- systemoriscatalyzedbyglucoseandATP-specificglucokinases,
chaealversions).Thepathwaymodificationsoccurmainlyinthe whereas in Eukarya, this reaction is catalyzed by ATP-specific
upper part of the archaeal pathways, involving ADP-, PP-, or hexokinases,whichusuallyshowbroadsubstratespecificityfora
i
ATP-dependent kinases, distinct from the classical enzymes in varietyofothersugars,likefructose,mannose,andgalactose(44,
BacteriaandEukarya.Also,thephosphoglucoseisomerasesaswell 45).Conversely,thebacterialATP-dependentglucokinasesshow
asthefructose-1,6-bisphosphatealdolasesinArchaeadifferfrom apronouncedspecificityfortheirrespectivesugarsubstrates(for
theirbacterialandeukaryoticcounterparts.Themoststrikingdif- literature,seereference 46).Boththeeukaryotichexokinasesas D
ferenceinarchaealpathways,especiallyin(hyper)thermophiles,is well as the bacterial glucokinases constitute distinct families o
w
the direct and irreversible oxidation of GAP to 3PG, catalyzed within the actin-like ATPase domain superfamily. Members of
n
either by NAD(P)(cid:3)-dependent nonphosphorylating glyceralde- thissuperfamilyshareasimilaroverallfoldconsistingofalarge lo
hyde-3-phosphate dehydrogenase (GAPN) or, mainly in anaer- domain(five-strandedmixed(cid:4)sheetfacedbyfive(cid:2)helicesonone a
d
obes,byferredoxin(Fd)-dependentglyceraldehyde-3-phosphate sideofthesheet)andasmalldomain(five-strandedmixed(cid:4)sheet e
oxidoreductase(GAPOR).Bothenzymesomittheformationof surroundedbythree(cid:2)helices,twoononesideandoneonthe d
f
1,3-bisphosphoglycerateandtheproductionofATPviasubstrate- othersideofthesheet).Theactivesiteislocatedatthedomain ro
levelphosphorylation,withconsiderableconsequencesforpath- interface,anduponsubstratebinding,theconformationchanges m
wayenergetics.Reducedferredoxin(Fd )canserveasanelec- toitsclosedstatethroughdomainmovement(44).Onthebasisof h
red t
tron donor in anabolic reactions instead of or at least in crystalstructures(47–49)andtheresultsofmutagenesisstudies tp
combination with NAD(P)H. The utilization of ferredoxin also (50),thecatalyticmechanismforsugarkinasesfromtheactin-like :/
/
allows for additional energy conservation via H generation by ATPasedomainsuperfamilyhasbeenproposedtoinvolveacon- m
2 m
meansofmembrane-boundhydrogenase,whichisespeciallyad- servedAsp(i.e.,Asp657inhumanhexokinaseI)thatabstractsthe
b
vantageous under anaerobic conditions. Despite the energetics, protonfromthe6-hydroxylgroupofglucoseasacatalyticbase. r
theEMPpathwaymodificationsinArchaeaalsostronglyinfluence Thisenablesanucleophilicattackofthe(cid:5)-phosphorusofATPon .a
s
theirregulation.TheclassicalsitesofallostericregulationinBac- theactivated6-oxygenofglucose,finallyyieldingG6P(seeFig.3). m
teria and Eukarya, i.e., particularly HK and ATP-PFK (PFK-A) ThepositivechargesofArg539andaMg2(cid:3)ionareproposedto .o
(seebelow),arereplacedinarchaealpathways.Also,thearchaeal stabilize the reaction intermediate. These catalytic residues are rg
PKsshowstronglyaltered(ifany)regulatoryproperties(seebe- structurally conserved in the sugar kinases of the actin-like /
o
low).Instead,asknownsofar,GAPN,mainlyfoundin(hyper)- ATPase domain superfamily. In Archaea, two different mecha- n

thermophilicArchaea,representsthemainsiteofallostericregu- nismsofglucosephosphorylationhavebeendescribed. M
lation. ADP-dependentglucokinase.InEuryarchaeotasuchasPyr.fu- a
r
Asoutlinedbelow,theunusualenzymesinthearchaealpath- riosus,Thermococcuslitoralis,andArc.fulgidus,glucosephosphor- c
h
waymodificationsrepresentmostlyexamplesofnonhomologous ylation is carried out by ADP-dependent glucokinases (ADP- 2
genereplacementsratherthannovelinventions(30).Incontrast GLKs).Theseenzymesshowhighspecificityforglucose(51–55) 8
,
tothemodificationsintheupperpartofthearchaealEMPvari- andbelongtotheribokinasesuperfamily.Conversely,intheCre- 2
0
ants,theenzymesinthelowerpart,withtheexceptionofcatabolic narchaeotaTpt.tenax,Pyrobaculumislandicum,Pyb.aerophilum,
1
GAPORandGAPN,i.e.,TIM,PGAM,ENO,andPK,arehomol- Aer.pernix,andDes.amylolyticus,thisprocessisATPdependent 9

ogoustotheirclassicalcounterpartsinBacteriaandEukarya.Also, (ADPforming),involvinganATP-dependenthexokinasewitha b
y
theGAPDH/PGKcouple,whichispresentinArchaea(exceptfor broad hexose substrate spectrum, as shown for the enzymes of g
extremehalophilesandsomemethanogens)exclusivelyforana- Aer.pernixandTpt.tenax(40,41,46,55).TheseATP-dependent u
e
bolicpurposes(seeGluconeogenesis,below),correspondswellto archaealhexokinasesbelongtotheROK(repressorprotein,open s
t
itsclassicalcounterparts.Furthermore,thephylogeniesofthese readingframe,sugarkinase)family(seebelow).Whereasclassical
universally distributed enzymes show distinct archaeal clusters, eukaryotichexokinasesrepresentmonomeric,andsometimesdi-
whereasthebacterialandeukaryoticproteinsappearedtobemore meric,proteins(subunitsizeof(cid:6)50or100kDa),andthebacterial
closelyrelatedandlessdistinct,presumablyduetoanendosym- ATP-dependentglucokinasesaredimerscomposedof(cid:6)30-kDa
biotic origin and lateral gene transfer events, respectively. The subunits,thearchaealADP-GLhavebeenbiochemicallycharac-
universaldistributionandhomologyoftheenzymesofthelower terizedasmonomericenzymes(subunitof(cid:6)50kDa)(44–46,51,
partoftheglycolysispathwayincombinationwiththeirlowevo- 53–56).
lutionary rates have been taken as a strong indication that the ArchaealADP-GLKspreferADPasthephosphoryldonorand
EMPpathwayevolvedinthegluconeogenicdirection(43). additionallyalsoutilizeCDPbutnotGDP,IDP,orUDP(57).The
Inthefollowingsections,wedescribestepbystepthearchaeal Arc.fulgidusenzymeappearstobespecificforADP(51,53,54).
biocatalystsoftheupperandthelowershuntsoftheEMPpathway The bifunctional ADP-GLK/PFK from Mca. jannaschii also uti-
incomparisontotheirbacterialandeukaryoticcounterparts,with lizesGDP(40%)inadditiontoADP(100%)and,lessefficiently,
specialreferencetostructuralandmechanisticcharacteristics(Ta- CDP (14%) (58). The crystal structures of archaeal ADP-GLKs
ble1givesanoverviewofalltheenzymesinvolvedinthemodified from Pyr. furiosus, Pyrococcus horikoshii, and Tco. litoralis have
94 mmbr.asm.org MicrobiologyandMolecularBiologyReviews
UniqueFeaturesofArchaealCarbohydrateMetabolism
beensolved,identifyingthearchaealADP-GLKsasmembersof andBac.subtilis)orhomotetramers(The.thermophilusandStr.
theADP-dependentsugarkinasefamilywithintheribokinasesu- griseus).SincemostbacterialROKkinaseswereshowntobespe-
perfamily (59–61). The basic fold of ADP-GLK is composed of cificfortheirrespectivesugarsubstrates,ithasbeendiscussedthat
onelargedomainandanadditionalsmalldomain,withtheactive thebroadsubstratespectrummightbeacharacteristicfeatureof
site located at the domain interface (Fig. 2A). The nucleotide archaealROKsugarkinases(63).However,theThe.thermophilus
bindingsitelieswithinthelargedomain,andthesugarbinding ROKsugarkinasealsoconvertsmannoseinadditiontoglucose
siteliesinacleftbetweenbothdomains.Thelargerdomaincon- (64).AlthoughnocrystalstructuresofarchaealROKkinasesare
sistsofatwisted11-to12-stranded(cid:4)sheetflankedonbothfaces available,thestructuresfromBacteriarevealedatwo-domainar-
by13(cid:2)helicesand33 helices,formingan(cid:2)/(cid:4)3-layersandwich. chitectureandfoldsimilartothosedescribedforhexokinasesand
10
Thesmallerdomain,whichcoverstheactivesite,formsan(cid:2)/(cid:4) ATP-dependent glycerate kinases (ATP-GKs), with both sub-
two-layerstructurecontaining5to7(cid:4)strandsand4(cid:2)heliceson stratesbindinginthecleftbetweenbothdomains(64,66).From
thefarsideoftheactive-sitecleftofthesheet(56,59–61).Thelarge theaminoacidsequencesimilarities,comparablestructuresmight
domainrepresentstheribokinasecorefold,whichtypicallycon- alsobeexpectedforthearchaealROKkinases.ThearchaealROK
sistsofaneight-stranded(cid:4)sheetsurroundedbyeight(cid:2)helices, hexokinaseactivitiesappearedtobedependentonbivalentmetal D
threeononesideandfiveontheothersideofthesheet(57).Upon ions (46, 55), and in the crystal structures of bacterial ROK ki- o
sugar binding, the small domain undergoes a conformational nases,aboundZn2(cid:3)ioninazincfingermotifhasbeenobserved w
n
change, closing the active site (59, 61). Although the “classical” (64, 66). This zinc ion interacts with residues that in turn are lo
hexokinasesinEukaryahavebeendescribedtopossessasimilar involvedinsubstratebinding,andthereby,thiszincionhelpsto a
d
two-domain architecture and to follow a comparable catalytic positionthesugarsubstrateforcatalysis.Thecatalyticmechanism e
d
mechanism, there are no similarities between ADP-GLKs and oftheROKkinasesseemstobesimilartothatdescribedforATP-
f
hexokinases either on the sequence level or in the fold of both GLKandHK(65).Althoughasimilarmechanismwasalsopro- ro
domains (44, 45, 57). ADP-GLKs contain two sequence motifs, posedforADP-dependentkinases(seeabove),therearenostruc- m
i.e., GXGD and NXXE, highly conserved in members of the ri- turalorsequencesimilaritiesbetweenbothenzymes,andalso,the h
t
bokinasesuperfamilyandinvolvedincatalysis(57).Theaspartate mechanismofmetaliondependencyappearstobedifferent(46, tp
residue of the GXGD motif has been proposed to act in sugar 50) (Fig. 2A and C and 3). In the crystal structure of the Bac. :/
/
bindingandasageneralbaseduringthecatalyticcycle(proton subtilisROKfructokinase,nodrasticconformationalchanges m
m
abstractionfromtheacceptorhydroxylgroup)(57,59)(Fig.3). havebeenobserveduponsubstratebinding.
b
AsparagineandglutamateoftheNXXEmotifareproposedtobe Otherarchaealsugarkinases.ForSulfolobustokodaii,ahexoki- r
.
involvedinbivalentmetalcationandnucleotidebinding(57,62). nase from the actin-like ATPase domain superfamily has been a
s
ADP-GLKsdependstrictlyonbivalentmetalions,whichcoordi- purified,andtheencodinggenehasbeenidentified(67).The64- m
natepropernucleotidebindingandpositioningofthephosphate kDadimericenzyme(subunitsof32kDa)showedabroadsub- .o
groupsforthephosphoryltransferreaction(51,53,54,57,62). stratespectrum,convertingmannose,glucosamine,N-acetylglu- rg
Recently,athirdmotif(HXE),withahighlyconservedglutamate cosamine(GlcNAc),and2-deoxyglucoseinadditiontoglucose, /
o
involvedinmetalioncoordination,hasbeenidentified.Further- withapreferenceforATPasthephosphoryldonor.ADPshowed n

more, binding of a second metal ion to another conserved se- aninhibitoryeffectontheenzyme.ThecrystalstructureofSul. M
quence motif in ADP-dependent sugar kinases with regulatory tokodaiiHK(StHK)showedahexokinase-likefold(Fig.2C)and a
r
implicationshasbeenproposed(62).However,alloftheADP- exhibited some sequence similarities with mammalian GlcNAc c
h
dependentsugarkinases,includingthosefromArchaeareported kinases,althoughthelatterenzymesarespecificforGlcNAc(49). 2
sofar,didnotshowanyregulatorypropertieslikecooperativityor HomologsofthisSul.tokodaiihexokinasewithsequencesimilar- 8
,
allosteric control, thus differing from eukaryotic hexokinases, itiesof(cid:7)50%wereidentifiedonlyinSulfolobusspecies.Dueto 2
0
whichrepresentoneofthesitesofallostericcontrolintheclassical theirfoldandsincetheseSulfolobusenzymesseemtobelongto
1
EMPpathway(56). neithertheROKnortheglucokinasefamily,ithasbeendiscussed 9

ROK hexokinase. The second mechanism of glucose phos- thattheyrepresentnewmembersofthehexokinasefamilywitha b
y
phorylation in Archaea is catalyzed by ATP-dependent kinases uniquesubstratespecificity. g
withbroadsugarsubstratespecificity,asdescribedforAer.pernix InhalophilicArchaea,amodifiedversionoftheEMPpathway u
e
and Tpt. tenax, which convert several other sugars in addition isusedforthedegradationoffructose,inwhichthesubstrateis s
t
to glucose, such as fructose, mannose, and 2-deoxyglucose phosphorylatedtofructose1-phosphate(F1P)viaketohexokinase
(46, 55). These (cid:6)35-kDa monomeric enzymes exhibit the (KHK).F1Pisfurtherphosphorylatedby1-phosphofructokinase
two signature patterns of the ROK family [LIVM]-x -G- (1-PFK)toF1,6BP,whichisthencleavedtoDHAPandGAPby
(2)
[LIVMFCT]-G-X-[GA]-X-G-X -[GATP]-X -G-[RKH] and fructose bisphosphate (FBP) aldolase (FBPA). DHAP and GAP
(3-5) (2)
C-X-C-GX -G-X-[WILV]-E-X-[YFVIN]-X-[STAG] (46). The areconvertedtopyruvatebyclassicalEMPpathwayenzymes(68–
(2)
ROKkinasesconstituteonefamilywithinthesuperfamilyofac- 70).TheKHKfromHaloarculavallismortiscatalyzingthefirststep
tin-likeATPasedomainproteinsalsocomprisingthehexokinase inthisEMPpathwaymodification,i.e.,theATP-dependentphos-
family and the ATP-dependent glucokinase family (see above) phorylationoffructosetofructose1-phosphate,hasbeenpurified
(44).InadditiontothearchaealROKhexokinases,severalROK andcharacterized(71,72).Thenativemolecularmasswasdeter-
sugarkinaseshavebeencharacterized(e.g.,fromThermotogama- minedtobe100kDa,butthesubunitcompositionandsizescould
ritima),andcrystalstructures(e.g.,fromThermusthermophilus, notunambiguouslybeestablished.F1P-formingKHKsareknown
Bacillussubtilis,andStreptomycesgriseus)havebeenreported(63– mainlyfromEukarya.TheseenzymesbelongtothePFK-Bfamily,
65).IncontrasttothemonomericarchaealROKkinases,thebac- as revealed by sequence and structural analyses, and represent
terialROKsugarkinasesrepresenthomodimers(Tmt.maritima (cid:6)70-kDadimericproteinscomposedofasingle(cid:6)35-kDasub-
March2014 Volume78 Number1 mmbr.asm.org 95
Bräsenetal.
ea Distribution EukaryaBacteria Archaea(mainlyanaerobicEuryarchaeota) Archaea(Crenarchaeota),BacteriaHalophilicEuryarchaeota,Eukarya Crenarchaeota(Sulfolobus) Eukarya,Bacteria,halophilicEuryarchaeota,methanogenicEuryarchaeota(Methanococcus)Crenarchaeota,Euryarchaeota(Thermoplasma) AnaerobicEuryarchaeota(includingMethanosarcinasomeBacteria(Ensifermeliloti,mazei),SalmonellaTyphimurium,horizontalgenetransfer)Eukarya,Bacteria Archaea,(mainlyanaerobicEuryarchaeota),glycogen-formingmethanogensCrenarchaeota(Aeropyrumpernix,Desulfurococcusamylolyticus)Crenarchaeota(Thermoproteustenax),someBacteria,Eukarya(protists,plants) Eukarya Archaea,Bacteria HalophilicEuryarchaeota,Bacteria,fungi Eukarya,Bacteria,Archaea Eukarya,Bacteria,halophilicEuryarchaeota,glycogen-degradingmethanogens(catabolicandanabolic),allotherArchaea(onlyanabolic) Eukarya,Bacteria,halophilicEuryarchaeota,glycogen-degradingmethanogens(catabolicandanabolic),allotherArchaea(onlyanabolic)
a
wellasinthemodifiedEMPpathwayversionsinArch Proteinsuperfamily(ies)(accordingtotheSCOPdatabase)Proteinfamily(ies) Actin-likeATPasesuperfamilyHexokinasefamilyActin-likeATPasesuperfamilyGlucokinasefamily RibokinasesuperfamilyADP-dependentsugarkinasefamilyActin-likeATPasesuperfamilyROKfamilyPFK-BProteinsequenceinArchaeaunknown;eukaryoteribokinasesuperfamilyActin-likeATPasesuperfamilyProbablyBadF/BadG/BcrA/BcrDATPasefamilyPGIsuperfamily(SISdomainPGIfamilysuperfamily)PGIsuperfamily(SISdomainPGI/PMIfamilysuperfamily)CupinsuperfamilycPGIfamily PhosphofructokinasesuperfamilyPhosphofructokinasefamily(knownasPFK-A)RibokinasesuperfamilyADP-dependentsugarkinasefamilyRibokinasesuperfamilyPFK-Bfamily PhosphofructokinasesuperfamilyPhosphofructokinasefamily(knownasPFK-A),formingadistinctsubfamily(cid:4)(cid:2)Aldolasesuperfamily[()ClassIaldolasefamilybarrel8fold] (cid:4)(cid:2)Aldolasesuperfamily[()ClassIaldolasefamilybarrel8fold] (cid:4)(cid:2)Aldolasesuperfamily[()ClassIIFBPaldolasefamilybarrel8fold] TriosephosphateisomeraseTriosephosphateisomerase(cid:4)(cid:2)superfamily[()familybarrelfold]8GAPDHN-andC-terminalN-terminaldomainNAD(P)bindingdomainfamilies,Rossmanfold-likedomainrespectivelysuperfamily;C-terminalglyceraldehyde3-phosphatedehydrogenase-like,C-terminaldomainsuperfamilyPhosphoglyceratekinasesuperfamilyPhosphoglyceratekinasefamily http://mmbr.asmDownloaded from
pathwayinBacteriaandEukaryaas Reaction(cid:3)¡(cid:3)HexoseATPhexose6-phosphateADP(cid:3)¡(cid:3)GlucoseATPglucose6-phosphateADP(cid:3)¡(cid:3)GlucoseADPglucose6-phosphateAMP(cid:3)¡(cid:3)HexoseATPhexose6-phosphateADP(cid:3)¡(cid:3)FructoseATPfructose1-phosphateADP (cid:3)¡(cid:3)HexoseATPhexose6-phosphateADP Glucose6-phosphatefructose6-phosphate% Glucose6-phosphate/mannose6-phosphatefructose6-phosphate%Glucose6-phosphatefructose6-phosphate% (cid:3)¡Fructose6-phosphateATPfructose1,6-(cid:3)bisphosphateADP(cid:3)¡Fructose6-phosphateADPfructose1,6-(cid:3)bisphosphateAMP(cid:3)¡Fructose6-phosphateATPfructose1,6-(cid:3)bisphosphateADP(cid:3)Fructose6-phosphatePPfructose1,6-%i(cid:3)bisphosphatePi Fructose1,6-bisphosphate%(cid:3)dihydroxyacetonephosphateglyceraldehyde3-phosphateFructose1,6-bisphosphate%(cid:3)dihydroxyacetonephosphateglyceraldehyde3-phosphateFructose1,6-bisphosphate%(cid:3)dihydroxyacetonephosphateglyceraldehyde3-phosphateDihydroxyacetonephosphate%glyceraldehyde3-phosphate(cid:3)(cid:3)(cid:3)Glyceraldehyde3-phosphateNAD(P)Pi(cid:3)(cid:3)1,3-bisphosphoglycerateNAD(P)H%(cid:3)H (cid:3)1,3-BisphosphoglycerateADP3-%(cid:3)phosphoglycerateATP on March 28, 201.org/
P 9
classicalEM Abbreviation HKATP-GLK ADP-GLK ROK-HKKHK HK PGI PGI/PMI cPGI ATP-PFK ADP-PFK PFK-B PP-PFKi FBPAI FBPAIA FBPAII TIM GAPDH PGK by gue
volvedinthe Cno. 7.1.17.1.2 7.1.147 7.1.17.1.3 7.1.1 3.1.9 3.1.9/5.3.1.8 3.1.9 7.1.11 7.1.146 7.1.11 7.1.90 1.2.13 1.2.13 1.2.13 3.1.1 (cid:3)2.1.13(NADP),1.2.1.12(cid:3)(NAD) 7.3.2 st
n E 2.2. 2. 2.2. 2. 5. 5. 5. 2. 2. 2. 2. 4. 4. 4. 5. 1. 2.
i
s
TABLE1Overviewofenzyme Enzyme HexokinaseATP-dependentglucokinase ADP-dependentglucokinase ROKhexokinaseKetohexokinase Hexokinase Phosphoglucoseisomerase Phosphoglucose/phosphomannoseisomeraseCupin-typephosphoglucoseisomerase ATP-dependentphosphofructokinase ADP-dependentphosphofructokinase ATP-dependentphosphofructokinase PP-dependentphosphofructokinasei Fructose-1,6-bisphosphatealdolaseclassI ArchaealtypeclassIfructose-1,6-bisphosphatealdolase Fructose-1,6-bisphosphatealdolaseclassII Triosephosphateisomerase Glyceraldehyde-3-phosphatedehydrogenase(phosphorylating) Phosphoglyceratekinase
96 mmbr.asm.org MicrobiologyandMolecularBiologyReviews
UniqueFeaturesofArchaealCarbohydrateMetabolism
a
n
GAPN hanosarci
(Hyper)thermophilicArchaea AnaerobicArchaea,someanaerobic(hyper)thermophilesinadditionto Vertebrates,yeasts,Bacteria,mainlythermoacidophilicArchaeaandMetspp.Plants,nematodes,Bacteria,Archaea Eukarya,Bacteria,Archaea Eukarya,Bacteria,Archaea Eukarya,Bacteria,Archaea
ALDH-likefamily Aldehyde:ferredoxinoxidoreductase,N-andC-terminaldomainfamilyCofactor-dependentphosphoglyceratemutasefamily2,3-Bisphosphoglycerate-independentphosphoglyceratemutase,catalyticdomainfamily;2,3-bisphosphoglycerate-independentphosphoglyceratemutase,substratebindingdomainfamilyEnolase-like,N-andC-terminaldomain-likefamilyPyruvatekinasefamily(N-terminaldomain);pyruvatekinasebetabarreldomainfamily(Cterminal)Pyruvate:phosphatedikinaseN-terminal,central,andC-terminaldomainfamilies,respectively(alsoknownasPEP-utilizingenzymefamily) Downloaded fr
o
ALDH-likesuperfamily Aldehyde:ferredoxinoxidoreductase,N-andC-terminaldomainsuperfamily Phosphoglyceratemutase-likesuperfamily Alkalinephosphatasesuperfamily;2,3-bisphosphoglycerate-independentphosphoglyceratemutase,substratebindingdomainsuperfamily Enolase-like,N-andC-terminaldomainsuperfamily PEP-pyruvatedomainsuperfamily;pyruvatekinasebeta-barreldomain-likesuperfamily GlutathionesynthetaseATPbindingdomain-likesuperfamily(N-terminaldomain)(ATPgraspfold);phosphohistidinedomainsuperfamily(centraldomain);phosphoenolpyruvate/pyruvatedomainsuperfamily(C-terminaldomain)(TIMbarrelfold) http://mmbr.asmm
.
(cid:3)(cid:3)¡Glyceraldehyde3-phosphateNAD(P)(cid:3)(cid:3)(cid:3)3-phosphoglycerateNAD(P)HH (cid:3)¡Glyceraldehyde3-phosphateFd3-ox(cid:3)aphosphoglycerateFdred 3-Phosphoglycerate2-phosphoglycerate% 3-Phosphoglycerate2-phosphoglycerate% 2-Phosphoglyceratephosphoenolpyruvate% (cid:3)¡(cid:3)PhosphoenolpyruvateADPpyruvateATP (cid:3)(cid:3)PyruvateATPP%i(cid:3)(cid:3)phosphoenolpyruvateAMPPPi on March 28, 2019org/

b
GAPN GAPOR dPGAM iPGAM ENO PK PPDK y gue
s
n. t
xi
o
d
1.9 7.6 2.1 2.1 1.11 1.40 9.1 ferre
1.2. 1.2. 5.4. 5.4. 4.2. 2.7. 2.7. uced
Glyceraldehyde-3-phosphatedehydrogenase(nonphosphorylating)Glyceraldehyde-3-phosphate:ferredoxinoxidoreductase 2,3-Bisphosphoglycerate-dependentphosphoglyceratemutase 2,3-Bisphosphoglycerate-independentphosphoglyceratemutase Enolase Pyruvatekinase Pyruvate:phosphatedikinase aFd,oxidizedferredoxin;Fd,redoxred
March2014 Volume78 Number1 mmbr.asm.org 97
Bräsenetal.
identifiedand,sincefructosewasshowntobetransportedintothe
cellsandphosphorylatedbyaPTS(seebelow)inHfx.volcanii,the
activityofKHKmightnotberequired.Nevertheless,inHaloar-
cula marismortui, KHK activity seems to be induced during
growthonfructose(70).
PhosphoglucoseIsomerase
Phosphoglucose isomerases (PGIs) catalyze the interconversion
of the aldose G6P to the ketose F6P in both the classical EMP
pathwayinBacteriaandEukaryaaswellasthemodifiedversions
inArchaea.Thisreactionisanintramolecularredoxreaction/elec-
tronrearrangementinwhichanaldehyde(C-1inG6P)isreduced
and the hydroxyl group at C-2 is oxidized to a ketone. This is
accompaniedbyaprotonrearrangement.ConventionalPGIsof D
o
EukaryaandBacteriafromavarietyofsourceshaveextensively w
beeninvestigated,andthecrystalstructureshavebeenreported n
forseveralorganisms(e.g.,pig,rabbit,human,andthebacterium lo
a
Bacillusstearothermophilus).Theconservedaminoacidsproposed d
e
to be involved in substrate binding and/or catalysis have been
d
identified(forliterature,seereference74).PGIsfrommammalian f
r
sourcesexhibitthepropertiesofacytokineinvolvedincellmigra- o
m
tionandproliferation(75,76).ConventionalPGIsarehomodi-

mericproteins((cid:6)120kDa),andeachsubunit((cid:6)60kDa)com- h
t
t
prises two domains. The active center located at the domain p
FIG2Ribbonrepresentationofthecrystalstructuresofthemonomersofthe interfaceismadeupofresiduesfrombothsubunits.Theconven- ://
differentsugarkinasesfoundinArchaea.(A)ADP-GLKfromPyr.furiosus m
tionalPGIsbelongtothePGIfamilywithinthePGIsuperfamilyof
(PDBaccessionnumber1UA4)(59)asarepresentativeoftheADP-dependent m
sugarkinasefamilywithintheribokinasesuperfamilyalsocomprisingADP- proteins(SIS[sugarisomerase]domainsuperfamilyintheSCOP b
PFKsaswellasthepromiscuousADP-GLK/PFKfromMca.jannaschii.(B) database)(45,77–80).InArchaea,homologsoftheseclassicalbac- r.
a
KDGKfromSul.solfataricus(PDBaccessionnumber2VAR)(122)asamem- terialandeukaryoticPGIshavebeenidentifiedonlyinhalophiles s
beroftheribokinasesuperfamily,exhibitingthePFK-BfoldliketheATP- m
andsomemethanogens,andtheenzymefromMca.jannaschiihas
dependentPFKspresentin,e.g.,Des.amylolyticusandAer.pernix.(C)HK .
beencharacterized(81).Instead,PGIactivityinallotherArchaea o
fromSul.tokodaii(PDBaccessionnumber2E2N)(49)asamemberofthe r
actin-ATPasedomain-likesuperfamilyalsocomprisingROKhexokinasesand isassociatedwithtwootherproteinfamilies. g
/
classicalHKsfromEukaryaandBacteria.(D)Classicalphosphofructokinase Phosphoglucoseisomerase/phosphomannoseisomerase.PGIs o
fromE.coli(PDBaccessionnumber6PFK)(101)asamemberofthePFK-A havebeenpurifiedfromAer.pernix,Tpt.tenax,andPyb.aerophi- n
family,towhichalsothePP-dependentPFKfromTpt.tenaxbelongs.All M
i lumaswellasfromthemodifiedEDpathwayutilizerTpl.acido-
illustrationsofcrystalstructureswerepreparedbyusingthePymolMolecular a
GraphicsSystem,version1.3(Schrödinger,LLC). philum(seebelow).Thecodingsequencesshowlowbutdetect- r
c
ablesequencesimilaritiestotheclassicalPGIs,especiallyinthose h

residuesinvolvedincatalysis(82–84).However,incontrasttothe 2
8
unit(73).IncontrasttothePFK-Bkinases(seebelow),evidence G6P/F6P-specificconventionalPGIs,thecorrespondingenzymes ,

that a phosphoenzyme intermediate is involved in the haloar- showpromiscuousPGIandphosphomannoseisomerase(PMI) 2
0
chaeal KHK catalytic cycle has been reported and no antigenic activities,convertingbothG6Pandmannose6-phosphate(M6P) 1
9
cross-reactivityusingantibodiesraisedagainsthaloarchaealKHK toF6P.SimilartotheclassicalPGIs,thearchaealPGI/PMIsare
b
couldbedetectedwithmammalianKHKfromdifferentrattissues dimersandshowatwo-domainstructure.Eachdomainshowsan y
(72).Thesefindingssuggestthatanovel,nonhomologousenzyme (cid:2)(cid:4)(cid:2)sandwichfold,whichisbuiltaroundaparallel(cid:4)sheet,five g
u
is involved in fructose phosphorylation in halophilic Archaea. strandedintheN-terminaldomainandfourstrandedintheC- e
However, the haloarchaeal KHK-encoding gene has not been terminal domain (Fig. 4). However, with a subunit size of (cid:6)35 s
t
FIG3Proposedreactionmechanismcatalyzedbysugarkinases,includingbase-mediatedprotonabstractionfromtheacceptorhydroxylgroupfollowedby
nucleophilicattackonthe(cid:5)-phosphategroupofATP.
98 mmbr.asm.org MicrobiologyandMolecularBiologyReviews