Diversity in Chemotaxis Mechanisms among the Bacteria and Archaea

19 Pages·2004·1.32 MB·English

MICROBIOLOGYANDMOLECULARBIOLOGYREVIEWS,June2004,p.301–319 Vol.68,No.2
1092-2172/04/$08.00(cid:1)0 DOI:10.1128/MMBR.68.2.301–319.2004
Copyright©2004,AmericanSocietyforMicrobiology.AllRightsReserved.
Diversity in Chemotaxis Mechanisms among the Bacteria
and Archaea
Hendrik Szurmant and George W. Ordal*
DepartmentofBiochemistry,CollegesofMedicineandLiberalArtsandSciences,
UniversityofIllinois,Urbana,Illinois61801
INTRODUCTION.......................................................................................................................................................301
SIGNALRECOGNITIONANDTRANSDUCTION..............................................................................................302
Receptors..................................................................................................................................................................302
Classesofreceptors............................................................................................................................................302
HAMPdomain.....................................................................................................................................................304
MethylationofclassIandIIIreceptors.........................................................................................................304
Structureofreceptors........................................................................................................................................305
Effectofattractantonstructure.......................................................................................................................305
MaturationbyCheD..........................................................................................................................................306
Bindingproteins..................................................................................................................................................306
Oxygensensing....................................................................................................................................................306
PhosphotransferaseSystem...................................................................................................................................306
EXCITATION..............................................................................................................................................................306
CheAKinase............................................................................................................................................................306
Couplingtoreceptors.........................................................................................................................................307
CheYResponseRegulator.....................................................................................................................................308
SignalAmplification...............................................................................................................................................309
ADAPTATION.............................................................................................................................................................309
Methylation..............................................................................................................................................................309
CheRmethyltransferase.....................................................................................................................................309
CheBmethylesterase..........................................................................................................................................310
Methylation-IndependentAdaptation..................................................................................................................311
CheVadaptationalandcouplingprotein........................................................................................................311
CheCdephosphorylatingandadaptationalprotein.......................................................................................311
SIGNALREMOVAL..................................................................................................................................................311
CheZPhosphatase..................................................................................................................................................313
CheC/FliY/CheXPhosphatase...............................................................................................................................313
PhosphateSink.......................................................................................................................................................313
MULTIPLECOPIESOFCHEMOTAXISGENES...............................................................................................313
LOCALIZATIONOFCHEMOTAXISPROTEINS...............................................................................................314
CONCLUSIONSANDPROSPECTS.......................................................................................................................314
ACKNOWLEDGMENTS...........................................................................................................................................314
REFERENCES............................................................................................................................................................314
INTRODUCTION type of signal transduction system in bacteria and controls
diverse processes such as gene expression, sporulation, and
The discovery of microbes by Antonie van Leeuwenhoeik
chemotaxis.Inchemotaxis,eventsatthereceptorscontrolau-
(59) was aided by their ability to swim, clearly indicating that
tophosphorylationoftheCheAhistidinekinase,andthephos-
theyarelivingorganisms.Notsurprisinglythemechanismcon-
phohistidineisthesubstratefortheresponseregulatorCheY,
trolling this behavior has since then been studied extensively.
whichcatalyzesthetransferofthephosphorylgrouptoacon-
Arguably,chemotaxisisthebestunderstoodofallsignaltrans-
servedaspartate(forarecentreview,seereference250).The
duction systems that control movement. While the motility
resulting CheY-P can interact with the switch mechanism in
apparatusdiffersamongorganisms,thegeneralcontrolmech-
the motor (42, 149, 186, 193, 234). This interaction causes a
anism is conserved throughout all bacteria and archaea. The
changeinbehavior,suchasindirectionorspeedofrotationof
centerpieceofthiscontrolmechanismisthe“two-component”
flagella. Thus, for example, in Bacillus subtilis, binding of the
system in which phosphorylation of a response regulator re-
attractant asparagine to the receptor McpB quickly increases
flects phosphorylation of a histidine autokinase that senses
thelevelsofCheA-PandCheY-P,astheexcitationevent,and
environmental parameters (117). This is the most common
produces increased counterclockwise (CCW) rotation of the
flagella (265). The receptors undergo adaptation, a feature
that allows the mechanism to reset so that bacteria can
*Correspondingauthor.Mailingaddress:DepartmentofBiochem-
istry,190Med.Sci.Building,UniversityofIllinois,Urbana,IL61801. progress up concentration gradients of attractants or down
Phone:[phone].Fax:[phone].E-mail:[email protected]. concentration gradients of repellents (152). In general, the
301
302 SZURMANT AND ORDAL MICROBIOL.MOL.BIOL.REV.
temsthathavebeenstudiedtodate.ThemainfocusisnotE.
colichemotaxis,sincemanyreviewarticleshavedealtwithits
chemotaxis, but Bacillus subtilis, which is arguably the second
best understood chemotactic bacterium. Other than cheZ, it
possessesatleastonecopyofeachchemotaxisproteinfoundto
date(althoughsomefusionsofchemotaxisproteinsexistthat
arenotfoundinB.subtilis).
As will become apparent, the chemotaxis mechanism in B.
subtilisisprobablyclosetothatoftheancestralorganismfrom
whichthebacteriaandarchaeadescended,sothatunderstand-
ing this mechanism should provide considerable insights into
mechanismsusedinthediversespeciesofmotilebacteriaand
archaea alive today. To appreciate the divergence in chemo-
taxis,wetriedtoincludeinthisreviewsomeinformationabout
at least one representative of each phylum of bacteria and
archaeainwhichaCheAhomologcouldbefound,indicating
the existence of a chemotaxis pathway. Of course, many or-
ganismshavenotyetbeenstudiedindetail,andtheavailable
information is often based only on the genomic sequence of
those organisms. We have made a special effort to include
information about organisms whose chemotaxis mechanism
appears to diverge from the E. coli paradigm. Other reviews,
most of which emphasize the E. coli mechanism, include ref-
erences13,39,61,224,and227.ThereviewbyBerg(20)does
justicetotheratherconsiderableliteraturedatingfromthelate
19thandearly20thcenturies.
FIG. 1. Generalchemotaxismodel.Aschematicofthebiochemical SIGNALRECOGNITIONANDTRANSDUCTION
processesinthetwo-componentchemotaxispathwayisshown.Hexa-
Receptors
gonsrepresentresponseregulatordomains.Theuniversalcomponents
areinred;almostuniversalcomponentsareinorange;optionalcom-
ponentsareinyellow. UnderstandinghowreceptorscontroltheCheAkinaseisat
the heart of understanding chemotaxis. In E. coli, binding of
attractantinhibitstheCheAkinase(34),whereasinB.subtilis,
bindingofattractantstimulatestheCheAkinase(64,67).Itis
excitationprocessishighlyconservedandthereisconsiderable important to understand the structure of receptors and how
varietyintheadaptationprocess(Fig.1). bindingofattractant(orrepellent)changestheactivityofthe
Besides these two core proteins, many other proteins con- associatedCheAkinase.
tribute to making the process work. Chemotaxis proteins can Classes of receptors. The receptors are usually transmem-
be ordered into four groups—a signal recognition and trans- brane proteins with an extramembrane sensing domain that
ductiongroup,anexcitationgroup,anadaptationgroup,anda binds attractant across the dimeric interface (253), two trans-
signalremovalgroup(todephosphorylateCheY-P).Thesignal membrane (TM) regions (TM1, between the N terminus and
recognition and transduction group includes the receptors (9, thesensoryregion,andTM2,betweenthesensoryregionand
81,118)andligandbindingproteins(4,86),whicharecapable the cytoplasmic regions), and several cytoplasmic regions.
ofbindingeffectorsoutsidethecell;afewreceptors,however, Theseincludethesignalingregion,wheretheCheAkinaseand
are cytoplasmic (92, 93, 229). The signal, i.e., changing con- the CheW coupling protein and analogs bind, and the meth-
centrationsofachemical,isthentransducedtotheexcitation ylationregion,wheremethylation/demethylationoftherecep-
proteins,CheAandCheY(34,90).Adaptationalproteinsalter torsoccurstocompensateforchangesinCheAkinaseactivity
CheA activity to reset the system. This can be done either by caused by binding attractant (Fig. 2). The enzymes catalyzing
influencing CheA activity directly or through the receptors. these reactions, the CheR methyltransferase and the CheB
Lastly, the signal removal proteins ensure that CheY-P levels methylesterase,aredescribedbelow.Betweenthemethylation
canbeadjustedtoprestimuluslevelsquickly(therolesofthe region and the membrane is the HAMP (histidine kinase,
chemtaxisproteinsaresummarizedinTable1). adenylyl cyclase, methyl-accepting chemotaxis protein, and
All biochemical processes described here were first discov- phosphatase) linker, which conveys the signal of attractant
ered in the enteric bacteria Escherichia coli and Salmonella binding to the rest of the cytoplasmic region (see below).
entericaserovarTyphimurium.Fortunately,theentericchemo- Based on crystal structures of the extramembrane N-terminal
taxissystemturnedouttobecomparativelysimple.Sincethen, partofTar,theaspartatereceptorofE.coli,andofthecyto-
chemotaxis in many diverse organisms has been studied and plasmic C-terminal part of Tsr, the serine receptor, virtually
many,oftencomplex,variationshavebeenfound.Thisreview theentirereceptoristhoughttoconsistmainlyof(cid:2)-helix(51,
aimstosummarizeandcomparethedifferentchemotacticsys- 108,109).
VOL.68,2004 BACTERIAL AND ARCHAEAL CHEMOTAXIS 303
TABLE 1. Listanddescriptionofproteinsinvolvedinchemotaxis
Proteinbycategory Activityorrole Comment Wherefound References
Signalrecognitionand
transduction
Methyl-acceptingchemotaxis Receptors Bindschemoeffectorsandtransduces Universalamongallchemotactic 9,33,46,56,75,104,109,
proteins(MCPs) signaltoCheA.Ismethylatedand bacteriaandarchaea 110,118,119,128,148,
demethylatedonglutamate 171,179,197,199,208,
residues. 213,215,229,237,241,
243,245,247,264,265
CheD Glutamine Roleinreceptormaturationby Allchemotacticarchaea,gram- 67,122,182
deamidase deamidationofparticular positivebacteria,Thermatoga,
glutamineresidues andsomeproteobacteria
Ligandbindingproteins Ligandrecognition Bindschemoeffectorsandtransduces E.coli,notyetknownforother 1,3,4,24,28,36,40,53,
signaltothereceptors. organisms 65,85,86,88,118,141,
157,158,165,166,256,
266
Excitation
CheA Histidinekinase Autophosphorylatesonhistidine Universalamongallchemotactic 23,33,64,67,70,90,137,
residue;substrateforCheYand bacteriaandarchaea 151,156,185,218,233,
otherresponseregulators. 264
CheW Couplingprotein CouplesCheAtothereceptors. Universalamongallchemotactic 37,70,78–80,131,144,
bacteriaandarchaea 187
CheY Response Primaryresponseregulator.Interacts Universalamongallchemotactic 16,25,26,35,49,209,
regulator withthemotilityapparatusto bacteriaandarchaea 211,218,244,259
inducechangeofswimming
behaviorwhenphosphorylated.
Adaptation
CheR Methyltransferase Methylatesglutamateresidueson Almostuniversalamong 47,48,116,182,214,264,
MCPs;roleinadaptation. chemotacticbacteriaand 265
archaea(exception,H.pylori)
CheB Methylesterase Hydrolyzesmethylglutamate Almostuniversalamong 10,45,57,73,74,90,102,
residuesonMCPs;rolein chemotacticbacteriaand 103,106,108,113,115,
adaptation.Usuallyhasresponse archaea(exception,H.pylori) 130,134,145,160,217,
regulatordomain. 219,220,226,264
CheV Couplingand CouplesCheAtothereceptors; ManybacteriaincludingtheE. 63,99,181
adaptational responseregulatordomaincanbe colicloserelativeS.enterica
protein phosphorylated;rolein serovarTyphimurium;however
adaptation. notinthearchaeaorE.coli
Signalremoval
CheC Phosphataseand HydrolyzesCheY-P;alsoprobable Allchemotacticarchaea,gram- 112,182,183,190
adaptational roleinadaptation. positivebacteria,Thermatoga,
protein andsomeproteobacteria
CheX Probable HomologoustoCheC,probablyhas Thespirochetes,somearchaea, 69,77,137
phosphatase thesamefunction. somegram-positivebacteria,
Thermatoga,andsome
proteobacteria
CheZ Phosphatase HydrolyzesCheY-P. The(cid:4)-and(cid:5)-proteobacteria 29–32,43,49,90,146,
188,189,195,223,257,
261
FliY Phosphataseatthe NterminushomologoustoCheC; Thegram-positivebacteria, 26,95,112,234
flagellarswitch hydrolyzesCheY-P;integralpart somespirochetes,and
oftheflagellarswitch. Thermatoga
CheY* Phosphatesink AlternativeCheYthatlowers The(cid:2)-proteobacteria,possibly 172,191,196,212
primaryCheY-Plevelsbyacting others
asaphosphatesink.
Le Moual and Koshland (124) showed that the chemotaxis divergedfromtheoriginallineandbeforetheproteobacterial
receptors in the bacteria and archaea fell into three classes, linehaddiverged,wasthedeletionofthefirstandfourthindels
based on the presence or absence of two pairs of insertions to produce the class II receptors. The class I receptors,
(called “indels,” for insertions/deletions) of 14 amino acids which involve deletion of indels 2 and 3, may have arisen
(fourturnsofthe(cid:2)-helix).TheclassIIIreceptorsarelikelyto several times, once during formation of the (cid:2)-proteobacte-
betheancestralreceptors(124).Thelocationsofthesepairsin rial line (see Rhodobacter sphaeroides), once during forma-
B. subtilis McpB are illustrated in Fig. 2. They lie on the tionofthe(cid:3)-proteobacterialline(seeMyxococcusxanthus),
membrane-proximal side of the signaling regions and methyl- once during formation of the (cid:4)-proteobacterial line (see
ationregions.TheclassIIIreceptorshavebothpairs,theclass Ralstoniasolanacearum),andonceafterthe(cid:5)-linehadbeen
II receptors have only the pair between the signaling and formed (see E. coli and Pseudomonas aeroginosa) (Fig. 3).
methylation regions, and the class I receptors have neither. Alternatively, and more probably, the class I receptors may
Morerecentanalysisofsequencesinthedatabase(Fig.3)gives havearisenfewertimesand,earlyduringtheevolutionofa
some additional perspective. The original receptors are obvi- particularlineofdescent,mayhaveenteredbygenetransfer
ouslytheclassIIIreceptors,buttheyhaveundergonemodifi- and displaced the original receptors. One obvious case of
cations early in the lines of descent. One modification, which gene transfer is in Clostridium acetobutylicum, a gram-posi-
presumablyoccurredafterthegram-positivebacteriallinehad tive bacterium having 38 class III receptors (all the rest of
304 SZURMANT AND ORDAL MICROBIOL.MOL.BIOL.REV.
FIG. 2. Schematic of the three classes of chemotaxis receptors. Shown is a representative dimer for each class of chemotaxis receptors.
Insertion/deletionregions(indels)areshadedindarkgray.Starsindicatesitesofmethylationfor(fromlefttoright)E.coliTar,M.xanthusFrzCD,
andB.subtilisMcpB.
the gram-positive bacterial receptors are class III) and one stimuli;methanolevolutioninthisspecieswassuppressedbe-
class I receptor (Fig. 3). The receptors in the spirochete lowbackgroundlevelsaftertheapplicationofpositivestimuli
Borreliaburgdorferi,heretermedclassO,areaspecialcase: (105, 241, 242). Interestingly, methanol is released from the
these receptors are missing indels 1 and 4 but are missing class I receptors of R. spheroides on addition of attractant
pairs of 21 amino acids where the loss of indels 2 and 3 (which, as in E. coli, inhibits CheA [196]) (145). There is no
would produce a loss of only a pair of 14 amino acids. consequence on methanol formation of removing the attract-
HAMP domain. As implied above, the HAMP domain or ant. However, as described below, this organism has multiple
linker is found in a number of different types of proteins. copies of chemotaxis genes. The principal methyltransferase
Although there is little sequence identity among HAMP do- appearstobeCheR2;deletionofcheR1causesmethanoltobe
mains,theygenerallyhavetwosegmentsofhydrophobicami- producedafterbothadditionandremovalofattractant(145).
noacylresiduesinaheptamericarrangementcharacteristicof Therelatedorganism,Rhodospirillumcentenum,however,be-
amphipathic(cid:2)-helicesjoinedbyunstructuredaminoacids(11, haved as might have been anticipated from the E. coli prece-
12). The (cid:2)-helices are probably in a coiled coil (206). The dent: a reduction of light intensity, which would cause inhibi-
purposeofHAMPdomainsisgenerallytoconveysignalsfrom tionoftheCheA,causedmethanolformation,andincreaseof
input domains to output modules. Mutations in the E. coli lightintensitydidnot(97).
receptorTsrHAMPdomaincausedlockedsignaloutput(that What is the reason for this difference in methanol forma-
is, persistently clockwise [CW] or CCW or in between, but tion? In E. coli, methylation of receptors increases CheA ki-
switchingrarely)(8). nase activity, an adaptational mechanism to compensate for
MethylationofclassIandIIIreceptors.Considerablework the decreased activity caused by attractant, and it does not
has been done on McpB from B. subtilis, which might be appear to matter which sites become methylated (106, 197,
considered a prototype for the class III receptors. The first 238).Bycontrast,eachofthesitesinMcpB,theoneclassIII
difference noticed between the class I and III receptors was receptorthathasbeencharacterizedinsomedetail,appearto
that methanol was released in response to all stimuli in B. have a different function. Glu630 is demethylated both after
subtilis (111, 240) and Halobacterium salinarum (163, 216) addition and removal of attractant (265) (provided that this
whereas it was released from E. coli, the prototype organism siteisinthemethylatedform).WhenitischangedtoAsp630,
for class I receptors, only after the application of negative whichcannotbemethylated(198),theresultingmutanthasa
VOL.68,2004 BACTERIAL AND ARCHAEAL CHEMOTAXIS 305
FIG. 3. Phylogenetictreeofchemotacticbacteriaandarchaea.Thephylogenetictreewasgeneratedfromthe16SrRNAsequencesbyusing
theprogramsCLUSTALWandDRAWTREE.Includedisinformationregardingthenumberandclassofchemoreceptorsforeachrespective
organism.ND,notdetermined.Organisms,byphylum,areasfollows:Archaea:Archaeoglobusfulgidus,Halobacteriumsalinarum,Methanosarcina
mazei, and Pyrococcus abyssi; Thermotogales: Thermotoga maritima; spirochetes: Borrelia burgdorferi, Leptospira interrogans, and Treponema
pallidum;cyanobacteria:NostocandSynechocystisspp.;gram-positivebacteria:Bacillussubtilis,Clostridiumacetobutylicum,Listeriainnocua,and
Thermoanaerobactertengcongensis;proteobacteria((cid:2)-subgroup):RhodobactersphaeroidesandSinorizhobiummeliloti;proteobacteria((cid:4)-subgroup):
Ralstonia solanacearum; proteobacteria ((cid:3)-subgroup): Myxococcus xanthus; proteobacteria (ε-subgroup): Helicobacter pylori; proteobacteria ((cid:5)-
subgroup):Escherichiacoli,Pseudomonasaeroginosa,andVibriocholerae.
lowprestimulusbias;whenattractantisadded,itadaptsonlyto caseofR.spheroidescontradictsthisrule).Noworkofthistype
the higher wild-type bias, and when attractant is removed, it hasbeendoneforanyclassIIreceptors.
hardly adapts at all (265). Glu637 seems crucial for causing Structure of receptors. The E. coli receptors are stable
adaptation to attractants, and only on removal of attractants dimers(153)arrangedastrimersofdimers(9).TheB.subtilis
doesmethanolevolvefromthatsite(providedthatthissiteis receptorsarealsosimilarlyarranged,and,infact,thetrimers
in the methylated form). Glu371 (encoded as Gln371 but de- ofdimersthemselvesinteractneartheouterpartofthecyto-
amidated(probablybyCheD[seebelow])doesnotplayarole plasmicmembrane(46),aspredictedbyKimetal.(110).X-ray
duringadaptationtoadditionorremovalofattractantbutmay structuresoftheextramembraneligandbindingdomainofthe
in some way be involved in being a regulator of methylation, E.colireceptorTar(194)andthecytoplasmicdomainoftheE.
since an mcpB Q371A mutant shows poor taxis to high con- coli receptor Tsr (109) are available, as well as of the ligand
centrationsofasparagine,similartoacheBmutant(seebelow) bindingdomainofthesoluble,cytoplasmicB.subtilisreceptor
(M.A.ZimmerandG.W.Ordal,unpublisheddata).Methanol HemAT,inthepresenceandabsenceofthenaturalligandO .
2
arises from Glu371 only on addition of attractant (provided The dimer that binds O (the form that stimulates the CheA
2
that this site is in the methylated form). Thus, in B. subtilis, kinase) is very symmetrical, and the dimer that is free of O
2
eachofthepositionsfromwhichmethanolariseshasadiffer- showsadistinctconformationalchangeintheTyr70ofoneof
ent function, and these functions, in the case of McpB (as thetwosubunitsofthedimer(254,255).Asdescribedindetail
stated above), cause methanol production from Gln(Glu)371 below, the CheR methyltransferase and the CheB methyles-
and Glu630 on addition of attractant and from Glu630 and teraseappeartobeespeciallyactiveonreceptorsthathavejust
Glu637onremoval(providedthatthesesitesareinthemeth- bound or released attractant and before the compensating
ylated form). The extent to which this rule about particular methylation changes have occurred that would help bring
siteshavingparticularfunctionsappliesgenerallyisnotknown; aboutadaptation.Thestructuralbasisofthisconformationof
further experiments are required, and one obvious organism increasedsusceptibilityisstillunknown(45).
withwhichtoexplorethisquestionwouldbeR.spheroides(see Effectofattractantonstructure.Onelongstandingquestion
previousparagraph).Inanycase,whathadseemeduntilnow hasbeenhowattractantinducesthereceptorstochangeCheA
the general rule that class III receptors produce methanol in kinase activity. In E. coli, attractant causes diminished CheA
response to all stimuli and class I receptors do so only in activity(35).BasedonevidencefromworkonCys-substituted
response to negative stimuli does not appear to be true (the receptors,whosecross-linkingisacceleratedbyoxidant,there
306 SZURMANT AND ORDAL MICROBIOL.MOL.BIOL.REV.
appears to be “downward piston” movement of TM2 of one betweenthechemotaxismachineryandthePrrsystem,which
monomerofthereceptordimer(50,94,123).Basedonexper- monitors electron flow through the alternative high-affinity
iments where the nitroxide spin label was attached to Cys cytochromeoxidase,cbb ,andpositiveaerotaxisbyinteraction
3
residuesinCys-substitutedreceptors,theextentofmovement with another, unknown sensor, both of which may operate
was deduced to be small, only about 1 A˚ (171). The effect of throughoneofthechemotaxiskinasesofthecell,CheA (180).
2
repellent on these receptors and the effect of attractant or Somespecies,forexampleSinorhizobiummeliloti,donotseem
repellent on class III receptors, such as McpB of B. subtilis, torespondtooxygeninthesamewaythatE.coliandB.subtilis
where attractant activates rather than inhibits the receptor do(bymodulatingthefrequencyofCCWversusCWrotation)
(67),isunknown. but, rather, change their swimming speed in response to oxy-
MaturationbyCheD.CheDisadeamidasethatdeamidates gengradients(263).
particularglutaminesintheB.subtilisreceptors(122),afunc-
tioncarriedoutbyCheBinE.coli.Mostchemotacticbacteria
PhosphotransferaseSystem
and archaea carry cheD. Therefore CheD is probably the an-
cestralmechanismofglutaminedeamidation.Theroleofthis
Thephosphotransferasesystem(PTS)helpsmediatetaxisto
function is not yet fully understood. However without CheD
a number of sugars and sugar alcohols in B. subtilis (68, 121,
the receptors are undermethylated and activate the kinase
169).Transportisrequired,butmetabolismisnot.Unliketaxis
poorly,indicatingthatdeamidationisnecessaryforactivation
to PTS sugars in E. coli, which does not require a specific
ofthereceptors(67,182).
receptorandworksevenwhenthemethylationsystemisinac-
Binding proteins. Although in most instances chemoeffec-
tivated by mutation (162) (but works poorly unless some re-
torsarethoughttointeractdirectlywiththereceptors,insome
ceptor is present [136]), chemotaxis to PTS substrates in B.
particular instances, specifically dedicated binding proteins
subtilisrequirestheC-terminalpartofMcpC(Fig.5).Inthese
bindthechemoeffectorandthecomplexthenbindstherecep-
experiments,chimerasbetweentheasparaginereceptorMcpB
tor. Thus, in E. coli, galactose binds to the galactose binding
and the proline receptor McpC revealed that the N-terminal,
protein(86),ribosebindstotheribosebindingprotein(4),and
extramembrane part of the receptors mediated amino acid
thecomplexbindstothereceptorTrg(83,87).Maltosebinds
taxis,asexpected,butonlytheC-terminalpartofMcpCcould
tothemaltosebindingprotein(85),andthecomplexbindsto
mediatetaxistoPTSsubstratesand,inparticular,themethyl-
theaspartatechemoreceptorTar(176).Itissuspectedthatthe
ation region appeared to be involved. The data were best
B.subtilisreceptorMcpCbindsattractantsindirectly,viabind-
interpreted by a model in which unphosphorylated enzyme I
ing proteins, since it mediates taxis to all amino acids except
interacted with McpC to bring about increased CheA activity
asparagine, some (such as proline and alanine) at very low
and adaptation occurred through the normal means (121).
concentrations (159, 168); however, no mutants in any such
Indeed,methanolwasproducedonadditionofglucose,asign
putativebindingproteinshavebeenidentified.
thatCheBwasstimulatedtohelpbringaboutadaptation(239).
Oxygensensing.TheoxygensensorinB.subtilisisHemAT,
In E. coli, since unphosphorylated enzyme I interacts with
whichishomologoustomyoglobin(92,93).Itissimilartothe
CheA (135), it is suspected that interaction of CheA with
repellent oxygen sensor, also termed HemAT, in the archeon
unphosphorylated enzyme I inhibits CheA. Large changes in
H. salinarum. It is a soluble receptor, having no transmem-
thelevelsofunphosphorylatedenzymeIcomparedwithphos-
braneregion,andhencesensestheinternaloxygenconcentra-
phorylated enzyme I occur during chemotactic excitation
tion. H. salinarum has another receptor for oxygen as an at-
(136). It would seem likely that the requirement for receptor
tractant.However,thisreceptorishomologoustocytochrome
found by Lux et al. (136) might be due to the inherent low
oxidaseofmitochondria(44)andhassixmembrane-spanning
activity of CheA in the absence of receptors (34) rather than
regions and may be a heme protein that also senses oxygen
theinteractionwithaspecificreceptor,asfoundforB.subtilis.
directly. Conversely, Aer, the oxygen sensor of E. coli, binds
flavinadeninedinucleotide(FAD)(21,22,177),andthesignal
caused by changing oxygen concentrations is probably medi- EXCITATION
atedbychangesinthelevelofreduction/oxidationofthisFAD
WiththeexeptionofMycoplasmaglidingmotility,itappears
(21, 177, 235, 236), a process involving a PAS domain in the
thatbacterialandarchaealmotilityisuniverselycontrolledby
receptor (178). Pseudomonas putida would appear to use the
thetwo-componentsystemoftheCheAkinaseandtheCheY
same mechanism (161). Tsr in E. coli also mediates oxygen
responseregulator.
taxis, perhaps by sensing changes in the proton motive force
acrossthecytoplasmicmembrane(177,204)butcertainlynot
bybindingoxygendirectly(Fig.4).
CheAKinase
Many other organisms perform aerotaxis (reviewed in ref-
erence236).Azospirillumbrasilense,an(cid:2)-proteobacterium,ac- Thecentralenzymethatmediatesinput,usuallyassensedby
cumulatesinanoxygengradientat3to5(cid:6)M.Atbothlower thereceptors,andcreatesanappropriatesignalforthemotor
andhighoxygentensions,theprotonmotiveforceislower,so is the CheA kinase. Attractants inhibit it in E. coli (34), S.
that it is assumed that both positive and negative aerotaxis, meliloti (192), and R. spheroides (196) and stimulate it in B.
which causes accmulation of bacteria at the optimum oxygen subtilis (67). As described in “CheY response regulator” (be-
tension,isduetosensingofchangesintheprotonmotiveforce low),itislikelythatforthearchaeaandthespirochetes,pos-
(262). R. sphaeroides also accumulates at an optimum oxygen itivestimuli(forinstance,chemoattractantsorattractantlight),
concentration. It shows negative aerotaxis due to interaction decreaseCheAactivity.Thus,B.subtiliswouldappeartobethe
VOL.68,2004 BACTERIAL AND ARCHAEAL CHEMOTAXIS 307
FIG. 4. Aerotaxisreceptors.Shownisaschematicofthefourknowntypesofaerotaxisreceptors.Indirectaerotaxisdefinesreceptorsthatdetect
oxygenlevelsbytheprotonmotiveforceorredoxstateofthecell.Directaerotaxisdefinesreceptorsthatdetectlevelsdirectlybyinteractingwith
oxygen.Blackdiamondsrepresenttheindicatedreceptorcofactors.
exception to this rather incompletely verified hypothesis that beingofconsiderablylowerenergy(K (cid:7)1.2(cid:8)104insteadof
eq
positivestimulidecreaseCheAactivity. 1inthereactionCheA(cid:1)ATP3CheA-P(cid:1)ADP)(66).When
Onactivation,CheAbecomesphosphorylatedonaparticu- E. coli becomes somewhat deenergized, it becomes smooth
lar histidine residue (His46 in B. subtilis and His48 in E. coli swimming (107), since CheA cannot be phosphorylated, and
[258]).CheAhasfivedomains(describedindetailinreference thusthebacteriumhasalarger“diffusionconstant”sothatit
23),andthisHisresidueislocatedwithinthefirst,P1orHpt, will leave the local environment by rapid translational move-
domain(156).Thefourth(P4)domainiswhereATPbindsand ment. However, when B. subtilis becomes somewhat deener-
catalysis occurs. The third (P3) domain is the dimerization
gized,thechemotaxissystemstillfunctions.Thus,thebacteria
domain, important since CheA is a dimer that transphospho-
donotbecometumbly(theconditionintheabsenceofCheY-P
rylates(232)(theP4regionofonemonomerphosphorylatesa
[27]) and thus unable to move away from the unfavorable
HisresidueintheP1domainoftheothermonomer).TheP5
environment but instead use chemotaxis to depart, a much
domainiswhereCheAcontactsthereceptorsandthecoupling
moreeffectiveprocessthanunregulatedsmoothswimming.In
protein, CheW. The P2 domain is where CheY and CheB,
termsofphylogeny,CheAfromB.subtilisclusterswithCheAs
which receive phosphoryl groups from CheA-P, dock (23, 89,
from archaea and spirochetes, apart from CheAs of the pro-
233). The exact mechanism of CheA autophosphorylation is
teobacteria(2).
notyetknown;however,severalconservedregionswithinthe
Couplingtoreceptors.CheAiscoupledtothereceptorsvia
P4 domain—the N-box, G1-box, F-box, G2 box, and GT-
block—areessentialforcatalysisinE.coliandarethoughtto CheW.CheWispresentinallbacteriathathavechemotaxisor
be involved in positioning of ATP into the active site (Fig. 6) phototaxis receptors. A second protein, CheV, which is a
(91). CheW-CheY fusion protein, is also capable of coupling the
CheA-PfromB.subtilisdiffersfromitsE.colicounterpartin kinasetothereceptorsandisdescribedbelow.CheVispresent
308 SZURMANT AND ORDAL MICROBIOL.MOL.BIOL.REV.
FIG. 5. PTSinchemotaxis.ThetwoknownchemotaxispathwaysforPTSsugarsareshown.TransportofPTSsugarsincreasestheconcentration
ofunphosphorylatedenzymeI(EI)thatcaneitherdirectlyinteractandinhibitCheA(receptor-independentsystem),asisthecaseinE.coli,or
indirectlystimulateCheAthroughthereceptors(receptor-dependentsystem),asthoughttobethecaseinB.subtilis.ThelettersA,B,andC
representcomponentsofanABCtransporter.Forbetterunderstanding,PTSproteinsareinyellow,B.subtilischemotaxisproteinsareinred,and
E.colichemotaxisproteinsareingreen.
inmanyeubacteria,includingS.entericaserovarTyphimurium, conserved aspartate residue by using CheA-P as a substrate.
a close relative of E. coli, but not in E. coli and not in any Thisprocessisthoughttoinvolveseveralconservedresidues—
archaea. In E. coli, CheW is required for activation of CheA twoaspartates,whichpositionanessentialMg2(cid:1)ion,alysine,
butnotforitsinhibition(7,35).CheWishomologoustotheP5 andathreonine(Fig.6)(132,244,260).Inflagellatedbacteria,
orregulatordomainofCheA(23). CheY-P interacts with FliM, shown for E. coli (248) and B.
subtilis (26, 234). In the spirochete Treponema denticola, mu-
tationofcheAblockedchemotaxisandcausedthebacteriato
CheYResponseRegulator
have few reversals of motion (137), implying that CheY-P
Theprimaryresponseregulatorthatgovernsthedirectionof causesreversalsofmotion.Toachievethis,itprobablybindsto
flagellarrotationisCheY-P(16,25,90)and,asimpliedabove, FliM, which is present in the spirochetes. The archeon H.
itcausesCCWflagellarrotationinB.subtilisandCWflagellar salinarumsimilarlyshowednoreversalsofmotionwhencheA
rotation in E. coli. It catalizes its own phosphorylation on a orcheYwasdeletedand,indeed,showedpreferentialforward
VOL.68,2004 BACTERIAL AND ARCHAEAL CHEMOTAXIS 309
FIG. 6. SchematicofCheAandCheY.ShownarethehistidinekinaseCheAandthegeneralresponseregulatorCheY.ForCheA,thefive
domainsarelabeledP1throughP5.ThephosphoreceivinghistidineinP1ishighlightedingray,andconservedregionswithindomainP4thatare
thoughttoplayanactiveroleincatalysisarealsohighlightedingray.ForCheY,conservedresiduesthatparticipateincatalysisarepositionedas
indicated.
swimming(chronicCWrotationoftheflagellaateachendof esterase” (below). Besides this, it seems likely that organiza-
thearcheon)(184).Thus,inthisorganism,CheY-Palsocauses tionofthereceptorsintoalatticecouldleadtoamplification;
reversals of motion and is required for CCW rotation of the in this arrangement, judicious methylation of receptors to in-
flagella. (Note: these are right-handed flagella [5], not the creaseCheAactivity(afterreductionofactivityfromattractant
morecommonleft-handedflagella[139]foundinE.coliandB. [in E. coli]) would allow this amplification to occur over a
subtilis,andtheflagellathemselvesaremoresimilartotypeIV broadrangeofattractantconcentrations(201,202).However,
pili [52] than to the flagella of bacteria.) There are no FliM it would appear that this alleged lattice quickly forms and
homologs in the archaea, and the site of the interaction of disappears, according to circumstances (see “Localization of
CheY-P to control the direction of flagellar rotation is un- chemotaxisproteins,”below).
known.Theimplicationofthesefindingsisthattheflagellaof
Halobacteriumandspirocheteshaveadefaultdirectionofro-
ADAPTATION
tation in the absence of CheY-P, as do the flagella in the
peritrichous bacteria like E. coli and B. subtilis, and that To sense ever higher concentrations of attractant and to
CheY-P not only facilitates rotation in the opposite direction movetowardfavorableenvironments,chemotaxissystemshave
butalsofacilitatesswitchingbetweenthetwodirections.How tobeabletoadapttoexistingstimuli.Additionally,thenature
this might occur is mentioned below (see “CheC dephospho- ofbacterialmotionrequirestheabilitytorecognizewhenthe
rylatingandadaptationalprotein”). bacterium is moving in the wrong direction, i.e., away from
higher attractant concentrations. To do that, a “memory” is
requiredthatisabletoindicatewhetherhigherorlowercon-
SignalAmplification
centrations are being reached (120). This is achieved by the
Bindingofoneortworeceptorsbyattractantcanleadtoa adaptational mechanisms. The methylation system of CheR
behavioralresponseinB.subtilis(113)andE.coli(195).Using and CheB is the only adaptational mechanism in E. coli that
photoreleasedaspartate,Jasujaetal.(96)foundthatnanomo- has been studied, although another, undescribed mechanism
larasparate(1.2(cid:6)MK )couldevokearesponseandthatthe mayexist(162,228).However,otherorganisms,e.g.,B.subtilis,
D
response times were proportional to changes in receptor oc- have at least partly characterized adaptational systems,
cupany near the threshold, irrespective of prior occupancy. namely,CheVandCheC(Fig.7),inadditiontothemechanism
(Therefore, adaptation is complete.) In experiments with E. involvingCheRandCheB(99,112).
coli, using fluorescence resonance energy transfer to measure
CheY-P levels (rather than CCW/CW rotation, which is a
Methylation
complex function of CheY-P levels), Sourjik and Berg (210)
found that the cheB mutant was very insensitive to attractant CheR methyltransferase. CheR methyltransferase transfers
compared to both the wild type and a cheR mutant. Using methylgroupsfromS-adenosylmethioninetoparticulargluta-
photoreleased asparate, Kim et al. (108) also found that the materesidues(102,164,238)onthereceptors(82,164),with
cheBmutantwasfarlesssensitivethanwasthewildtype.Both productionofS-adenosylhomocysteine(47,48,214).InB.sub-
groups found that absence of CheZ, which catalyzes the de- tilis,itisrequiredforadaptationtorepellents.Initsabsence,B.
phosphorylationofCheY-P,hadlittleeffectonamplification; subtilisisverytumbly(withpredominantlyCWrotationofthe
therefore,acceleratedlossofCheY-Pisnotthecauseofsignal flagella) (116). In E. coli, it is required for adaptation to at-
amplification; it must be sought in signal generation. How tractants (76, 119) and binds both to a flexible tether at the
CheBmightbeinvolvedinthisisdescribedin“CheBmethyl- C-terminalendofthereceptorandtothemethylationregion
310 SZURMANT AND ORDAL MICROBIOL.MOL.BIOL.REV.
FIG. 7. Adaptationsystems.Aflowchartofthepossiblemeansofadaptationisshown.Thealmostuniversalmethylation-dependentadaptation
systemisshownontheleft.Thelesshighlyconservedmethylation-independentpathwaysareontheright.WespeculateherethatCheVmight
directly influence CheA activity following phosphorylation, as shown, while the means of CheC activation and adaptational action are not yet
understood.Blackdiamondsrepresentachemoeffector.Adaptationalproteinsarehatched;excitatoryproteinsareshaded.
of the same or a nearby receptor and so moves through a enzymatic domain complements a null cheB mutant, and this
receptor cluster in a hand-over-hand fashion (58, 127, 252). strain(nullcheBmutanthavingtruncatedcheBonaplasmid)
This property, as might be expected, allows CheR bound to releases enhanced levels of methanol on both addition and
onereceptortomethylateanother(125,126,129),andrecep- removal of attractant. This result implies that the demethyl-
torslackingtheC-terminalbindingsitearepoorlymethylated ation reaction involves primarily the existence of a suitable
unlessreceptorscontainingitarepresentinthesamecell(19). substrate. The value of phosphorylation of CheB would then
ThepropertiesofE.coliCheRandB.subtilisCheRarelikely be to increase the rate of receptor demethylation and thus
to be similar since receptors of either organism can be meth- speed up adaptation and to minimize unnecessary receptor
ylatedbyCheRfromeitherorganism(47).CheRispresentin demethylation, since loss of a methyl group is equivalent to
virtuallyallbacteriaandarchaeashowingchemotaxis,sinceit hydrolyzing11to14ATPmoleculestoADPandP (45,225).
i
isimportantforadaptation;theexceptionisHelicobacterpylori, Interestingly,CheBfromCampylobacterjejunilacksaresponse
whichhasCheV,whosephosphorlation,asdescribedbelow,is regulator domain (142). It is assumed that the time during
knowntohelpbringaboutadaptationinB.subtilis(99). which enhanced methanol formation occurs is the time be-
CheB methylesterase. Unlike CheR, CheB is usually regu- tweenadditionorremovalofattractantandtheresultingcom-
lated;ithasanN-terminalresponseregulatordomain,subject pensating (to bring about adaptation) methylation events on
to phosphorylation, and a C-terminal enzymatic domain (57, thereceptor.Thisparticularsusceptibleconformationdoesnot
90,134,221).TheE.colienzymeis10-foldmoreactivewhen requirethecouplingproteinsCheWorCheVforeventsafter
phosphorylated (134). The B. subtilis enzyme can satisfy the the addition of attractant but does require them for events
requirementformethylesteraseforchemotaxisinE.coli(115), aftertheremovalofattractant(45).Thefactthatthereceptors
and, in vitro, both enzymes were able to demethylate both B. that have bound attractant are more susceptible to methyles-
subtilis and E. coli receptors (160). One interesting possible terasewasshowninvitromanyyearsago(160).
differenceisthatCheBdeamidatesparticularE.colireceptors, The methylation system, involving CheR and CheB, is im-
afterwhichthesitecanbemethylatedanddemethylated(102). portantforchemotaxistohighconcentrationsofattractantand
IntheinstanceswhereB.subtilisreceptorsaredeamidated(for only peripherally for chemotaxis to low concentrations of at-
instances where the reaction has been characterized), this re- tractant in B. subtilis (113, 115). The reason is thought to be
actioniscatalyzedbyCheD,notbyCheB(122).Perhaps,then, that at low concentrations of attractant, signal amplification
itisnotsurprisingthattheB.subtilisCheBappearstobemore occurs since binding attractant to a receptor activates neigh-
closelyrelatedtoCheBinthearchaea,whichhaveCheDand boring receptors (203). At high concentrations of attractant,
class III receptors, than to CheB in most bacteria, some of without CheB to generate charge-charge repulsion, there are
whichlackCheDand,inthecaseoftheproteobacteria,have no available free receptors that can activate the kinase on
classIandclassIIreceptors(2). binding attractant (113). At low concentrations of attractant,
The isolated enzymatic domain of CheB catalyzes receptor methylation-independent systems suffice to bring about adap-
demethylationinB.subtilis(45)andinE.coli(134),although tation,suchastheCheVsystem(seebelow).Thus,itmaynot
not as effectively as does the phosphorylated whole enzyme be surprising that the amount of methanol evolved increases
(10,57).However,inB.subtilis,atruncatedcheBencodingthe exponentiallywithreceptoroccupancybyattractant(111).