Stimulus Perception in Bacterial Signal-Transducing Histidine Kinases

29 Pages·2006·1.12 MB·English

MICROBIOLOGYANDMOLECULARBIOLOGYREVIEWS,Dec.2006,p.910–938 Vol.70,No.4
1092-2172/06/$08.00(cid:1)0 doi:10.1128/MMBR.00020-06
Copyright©2006,AmericanSocietyforMicrobiology.AllRightsReserved.
Stimulus Perception in Bacterial Signal-Transducing Histidine Kinases
Thorsten Mascher,1* John D. Helmann,2 and Gottfried Unden3*
DepartmentofGeneralMicrobiology,Georg-August-UniversityGo¨ttingen,D-37077Go¨ttingen,Germany1;Departmentof
Microbiology,CornellUniversity,Ithaca,NewYork14853-81012;andInstituteofMicrobiologyand
WineResearch,Johannes-Gutenberg-UniversityMainz,D-55099Mainz,Germany3
INTRODUCTION.......................................................................................................................................................910
PERIPLASMIC-SENSINGHISTIDINEKINASES...............................................................................................912
PrototypicalPeriplasmic-SensingHistidineKinases.........................................................................................915
NarX/NarQ-LikeSensorsofEnvironmentalNitrateandNitrite....................................................................919
CitrateandC -DicarboxylateSensorProteinsCitAandDcuS.......................................................................919 D
4
ProposedmodeofsignalperceptionandtransductionbyDcuS/CitA........................................................920 o
w
SensorKinaseswithPBPbSensingDomains.....................................................................................................920
n
NovelConservedPeriplasmicSensingDomains:CACHE,CHASE,andReg_prop.....................................921 lo
GeneralRolesofExtracytoplasmicSensorDomainsinStimulusPerception...............................................921 a
d
HISTIDINEKINASESWITHSENSINGMECHANISMSLINKEDTOTHETRANSMEMBRANE
e
REGIONS............................................................................................................................................................922 d

Intramembrane-SensingHKs:CellEnvelopeStressSensorswithTwoTMR(LiaS/BceS-LikeHKs).......922 f
r
LiaS-likeHKs......................................................................................................................................................923 o
m
BceS:atwo-componentsystem–ABCtransporterconnection......................................................................923

MiscellaneousIMHKs........................................................................................................................................923 h
t
IMHK-likeperiplasmic-sensingHKs:VanS/PrmB-likeproteins.................................................................923 tp
DesK-LikeThermosensorswithFourtoSixTMR............................................................................................923 :/
/
RegB/PrrB-LikeRedox-RespondingGlobalSensorKinaseswithSixTMR..................................................924 m
PeptideQuorumSensorswith6to10TMR(AgrC/ComD-,ComP-,andLuxN-LikeHKs).......................924 m
CbrA-andPutP-LikeProteinswithMorethan10TMR:SensorKinaseswithFusedSecondaryCarrier b
r
Domains...............................................................................................................................................................925 .a
NovelConservedPutativeTMR-AssociatedSensingDomainswithSixtoEightTMR:MHYT,MASE1, s
m
7TMR-DISM,and5TMR-LYT..........................................................................................................................926
.
ModelsforStimulusPerceptionAssociatedwithTMR....................................................................................926 o
r
CYTOPLASMIC-SENSINGHISTIDINEKINASES..............................................................................................927 g
/
Membrane-AnchoredHKswithN-TerminalCytoplasmicSensingDomains................................................927 o
Membrane-AnchoredHKswithC-TerminalCytoplasmicSensingDomains................................................928 n

SolubleHKsAssociatedwithMembrane-IntegralSensoryProteins..............................................................929 A
p
Soluble,Cytoplasmic-SensingHKs......................................................................................................................930 r
SolubleCytoplasmic-SensingHKs:the“MissingLink”betweenTwo-ComponentandOne-Component il
4
SignalTransduction?.........................................................................................................................................930 ,

COMBINATIONOFSENSINGDOMAINS...........................................................................................................931 2
0
CONCLUSIONSANDOUTLOOK..........................................................................................................................931 1
ACKNOWLEDGMENTS...........................................................................................................................................932 9

ADDENDUMINPROOF..........................................................................................................................................932 b
y
REFERENCES............................................................................................................................................................932
g
u
e
INTRODUCTION compounds, is a prerequisite for survival. For that purpose, s
t
bacteriahaveevolvedsurface-exposedsignaltransductionsys-
Life in the microbial world is characterized by continuous
tems, typically comprised of transmembrane (TM) proteins
interactions between the bacterial cell and its environment.
that channel the input from sensory modules to intracellular
Theabilityofabacteriumto monitor environmental param-
responses.TheseTMsignalingsystemsincludethechemotaxis
eters,includingosmoticactivityandionicstrength,pH,tem-
receptors, anti-(cid:2):(cid:2) factor pairs, Ser/Thr protein kinases, and
perature, and the concentrations of nutrients and harmful
histidineproteinkinasestogetherwiththeircognateresponse
regulators.Thisreviewfocusesontheclassicaltwo-component
systems(TCS)consistingofausuallymembrane-boundsensor
*Corresponding author. Mailing address for Thorsten Mascher:
histidineproteinkinase(HK)andaresponseregulator(RR),
Georg-August-University,Dept.ofGeneralMicrobiology,Grisebach-
str.8,D-37077Go¨ttingen,Germany.Phone:[phone].Fax: mostoftenmediatingdifferentialgeneexpression(103,108).
49 (0) 551-393808. E-mail: [email protected]. Mailing address for TCSallowadaptationalresponsestoahugevarietyofenvi-
Gottfried Unden: Johannes-Gutenberg-University, Institute of
ronmental stimuli, based on a simple modular system. Both
Microbiology and Wine Research, Becherweg 15, D-55128 Mainz,
proteins consist of (at least) two distinct domains. The HK
Germany. Phone: [phone]. Fax: [phone].
E-mail:[email protected]. harbors an N-terminal input domain that senses a specific
910
VOL.70,2006 STIMULUS PERCEPTION IN SIGNAL-TRANSDUCING HKs 911
stimulus,e.g.,bybindingorreactingwithasignalingmolecule cytoplasmicallylocated(87,280).Aclassificationbasedonthe
or by interaction with a physical stimulus. The information is Hboxofthekinasedomain(containingtheconservedsiteof
transduced through intramolecular conformational changes, autophosphorylation) was proposed by Fabret et al. (59) and
resulting in the activation of the cytoplasmic transmitter do- has found widespread use. The most comprehensive and de-
main (280). The transmitter, in turn, activates its cognate re- tailedsequenceanalysis,basedonallsixconservedboxes(the
ceiver,encodedbytheN-terminaldomainoftheRR.TheRR H, X, N, D, F, and G boxes) (see Fig. 2) in the transmitter
givesrisetotheappropriatecellularresponse,whichismedi- domain(87),allowsanevenmoreprecisesubgroupingofHKs.
atedbytheC-terminaleffector(oroutput)domainoftheRR A more recent classification (140), based on the sequence,
through protein-protein interaction (e.g., chemotaxis) or pro- organization,andpredictedsecondarystructureoftheHbox,
tein-DNAinteractionsleadingtodifferentialgeneexpression. allowed the classification of archaeal HKs for the first time.
The functional state of these two components is controlled Theseclassificationschemesarestillevolving,asevidencedby
by three phosphotransfer reactions: (i) the autophosphoryla- therecentidentificationofanewsubfamilyofHKs,theHWE
tionofaconservedhistidineinthetransmitterdomainofthe family(133).Althoughtheseanalyseshavefocusedspecifically
sensor, (ii) the phosphotransfer to a conserved aspartate in on the conserved features of the HK catalytic domain, they
D
thereceiverdomainoftheRR(bytheactivityoftheRR),and likelyreflecttheevolutionoftheTCSasawhole:inmanycases
o
(iii)dephosphorylationoftheRRtosetthesystembacktothe specific subfamilies of HK are preferentially associated with w
prestimulus state (202, 246). The phosphatase can be an in- specific subfamilies of RR proteins (87, 149). However, these n
trinsic property (autophosphatase) of the RR or a phospho- classifications neglect functional aspects of the sensing and lo
a
proteinphosphataseactivityofthekinasetowardstheregula- signaltransductionprocess. d
e
tor. However, external phosphatases are also common (129, The principal biological function of TCS-mediated signal d
205, 206, 246). Some HKs show significant autophosphatase transduction manifests itself in the input (signal perception) f
r
activitytowardstheirownHis-phosphategroup.Additionally, and output (e.g., differential gene expression), rather than in o
m
some RRs also catalyze significant back transfer of the phos- the communication between its two components. Therefore,
h
phategrouptothecorrespondingHiskinase(52). grouping HKs according to their input domains would reflect t
t
Withafewexceptions(i.e.,Mycoplasmaspecies),allbacte- the biological role they play in the communication between a p
:
/
rialgenomessequencedsofarharbormultiplecopiesofgenes cell and its environment. While a number of novel conserved /
m
encodingTCS.Typically,thestructuralgenesfortheHKand inputdomainswereidentifiedinHKsinrecentyears(5–7,65, m
the cognate RR are organized in operons. In some bacteria, 67,68,186,203,288,289),anoverallclassificationbasedonthe b
r
however,thetwo-componentsystemsshowanorphanorgani- N-terminal sensor domains remains problematic, since these .
a
zation at the gene level which impedes assigning sensor/regu- domains vary greatly in sequence, membrane topology, com- s
m
lator pairs and the identification of stimuli. This problem is position,anddomainarrangement.Allofthesefeatureshave
.
prominentinMyxococcusxanthus,whichcontainsalargenum- profound effects on sensing and signal transduction to the o
r
g
berofTCS(146HKs,includinghybridkinases),manyofwhich kinase domain. Therefore, this variability presumably reflects
/

are important for the control of complex differentiation pro- different principles in stimulus perception and processing, o
n
gramssuchasfruitingbodymorphogenesis.Morethan50%of whicharerelatedtothetopologyandtypeofsensorydomains
A
thestructuralgenesfortheHKsareorphansandareseparated but do not necessarily reflect the phylogenetic relationship of p
bytwoormoregenesfromthoseofthenextRR(238). thesensorkinases.Consequently,afunctionalclassificationof ril
Whilesomesystemshavebeenstudiedingreatdetail(most HKscannotbebasedonsequencealignmentsalonebutrather 4
,
notably the paradigmatic systems EnvZ/OmpR, CheA/CheY, requires the identification of domains and transmembrane 2
andNtrB/NtrCinEscherichiacoli)(25,109,187)andtranscrip- helices and the prediction of the topological arrangement of 0
1
tome approaches have allowed initial genome-wide investiga- thesestructures. 9

tions on some TCS, many are still uncharacterized. Genome- In order to arrange the large number of HKs according to b
y
widesequenceanalysestoidentifyTCShavebeenperformed functionalaspects,thesensorsaregroupedhereonthebasisof
g
for many bacteria, including Bacillus subtilis (59), Escherichia theirdomainarchitecture,i.e.,membranetopology,numberof u
e
coli(178),Pseudomonasaeruginosa(223),Corynebacteriumglu- TM helices, and sequential arrangement of the sensory do- s
t
tamicum(146),Streptomcyescoelicolor(107),andcyanobacte- main(s) within their N-terminal input domains. The available
ria (16). These analyses have been complemented, in some data clearly indicate that grouping HKs by these criteria is
cases, by mutational and/or microarray approaches, as re- functionally related to the mechanism of sensing and signal
ported for B. subtilis (145), Streptococcus pneumoniae (153, transductionbythecorrespondingsensorsbutdoesnotneces-
255), and E. coli (196, 286). It is anticipated that ongoing sarily take into account phylogenetic aspects. Based on our
functional genomics approaches will rapidly advance our un- analysis of the domain architecture and membrane topology
derstandingoftheselargesuitesofsensorysystems. of (cid:3) 4,500 sensor kinase sequences in the SMART database
SequencecomparisonsofTCShavebeenusedtoidentifya (229)(http://smart.embl-heidelberg.de/)andthepublishedre-
numberofconservedsubfamilies.Astructuralclassificationof sultsonsignalperceptionpresentedhere,most(ifnotall)HKs
bacterial response regulators based on the diversity of output fallintothreemajorgroups(Fig.1).
domains, domain architecture, and domain combinations was Thelargestgroup,theperiplasmic(orextracellular)-sensing
recently published (66). So far, comparisons of HK proteins HKs, includes proteins with an extracellular sensory domain
have focused on their highly conserved intracellular catalytic which is framed by at least two TM helices (Fig. 1A). The
(transmitter)domains(53,87,140).Theyshowahomogenous kinase is localized in the cytoplasm (as for all other HKs).
composition of subdomains (or “boxes”) and are generally Thus,sensoryandkinasedomainsarelocatedintwodifferent
912 MASCHER ET AL. MICROBIOL.MOL.BIOL.REV.
FIG. 2. Features,domains,andboxesofhistidineproteinkinases.
The protein is symbolized by the gray line. The major domains are
indicatedbyboxes,andtheirnamesaregivenaboveorbelowtheline.
Conserved boxes or amino acid residues are given below the line in
one-lettercode,accordingtothestandardnomenclature(87,280).The
drawingisnottoscale.SeethetextandTable1fordetails.
D
o
The subgroups within these three principal groups of HKs w
andtheircompositionsofdifferentsensorydomains,aswellas n
lo
the stimulus perception mechanisms for well-characterized
a
FIG. 1. Schematic representation of the three different mecha- representatives from each group, will be the subject of the d
e
nismsofstimulusperception.(A)Periplasmic-sensingHKs.(B)HKs followingsectionsofthisreview.Itshouldbepointedoutthat d
withsensingmechanismslinkedtothetransmembraneregions(stim- all classes of sensors can contain, in addition to the principal f
r
ulusperceptioncanoccureitherwiththemembrane-spanninghelices o
features (Fig. 2), additional sensory or linker domains in var-
alone or by combination of the transmembrane regions and short m
extracellular loops). (C) Cytoplasmic-sensing HKs (either soluble or iouscombinations.Wealsoaddressthemechanismofintramo- h
membrane-anchored proteins). The stimulus is represented by a red lecularTMsignaltransductionandtheoccurrenceandbiolog- t
t
arrow or red star. The parts of the proteins involved in stimulus ical role of HKs that harbor more than one putative stimulus p
:
perceptionarehighlightedincolor. perceptiondomain. //m
m
b
PERIPLASMIC-SENSINGHISTIDINEKINASES
r
cellular compartments which are separated by a membrane, .
a
necessitating TM signal transduction. This type of membrane Periplasmic-sensing HKs represent the classical type and s
m
topologyistypicalforsensingsolutesandnutrients. comprise the largest group of membrane-bound sensor ki-
.
The second group contains HKs with sensing mechanisms nases.Asadefinitionandforreasonsofsimplicity,weusethe o
r
g
associated with the membrane-spanning helices. The unifying term “periplasmic-sensing” HK throughout this review for all
/

feature of this highly diverse group of sensor kinases is the sensorkinaseswithasignificantlylargeextracytoplasmicinput o
n
presenceof2to20transmembraneregions(TMR)implicated domain,irrespectiveoftheirorigin(i.e.,HKsfrombothgram-
A
insignalperception.TheseTMRareconnectedbyveryshort negative and gram-positive bacteria). At present, databases p
intra-orextracellularlinkers;i.e.,thesesensorslackanobvious containabout2,500membersofthistype.Theyconsistoftwo ril
extracellular input domain (Fig. 1B). Therefore, the stimuli regions:anN-terminalperiplasmicsensingdomainflankedby 4
,
sensedeitheraremembraneassociatedoroccurdirectlywithin TMhelicesoneitherside(TMR1andTMR2),followedbythe 2
the membrane interface. Stimuli from within the membrane C-terminalcytoplasmictransmitterdomain(Fig.2).Thetrans- 0
1
includethemechanicalpropertiesofthecellenvelope(suchas mitterdomaincomprisesasequencewiththeconservedhisti- 9

turgor or mechanical stress) or are derived from membrane- dine residue for autophosphorylation (the H box) and ends b
y
bound enzymes or other membrane-integral components. with the highly conserved kinase (or catalytic) domain. The
g
Other membrane-related stimuli include ion or electrochemi- domain with the conserved His residue typically contains two u
e
cal gradients, transport processes, and the presence of com- (cid:4)-helices(Xbox),whichserveasadimerizationdomain(DHp s
t
pounds that affect cell envelope integrity. Most quorum sen- [dimerization and histidine phosphotransfer] or HisKA do-
sors from gram-positive bacteria also fall into this category. main) (Table 1 and Fig. 2). The catalytic domain (HATPase)
Forthelattergroup,twooftheTMRareconnectedbyashort containstheconservedN,D,F,andGboxeswiththerespec-
(20 to 50 amino acid residues) intra- or extracellular linker, tive highly conserved amino acid residues. This domain cata-
which seems to be involved in stimulus perception. Signal lyzesautophosphorylationoftheHKs.TheRRsthencatalyze
transferoccursfromthemembranetothecytoplasmickinase their own phosphorylation, with the phosphoryl-HK as the
domain. phosphodonor(279,280).Insomecases,low-molecular-weight
Thethird(andsecond-largest)groupofsensorkinases,the donors such as acetyl phosphate or, in vitro, also phosphor-
cytoplasmic-sensingHKs,includeseithermembrane-anchored amidatescanbeusedforRRphosphorylation(45,158).
or soluble proteins with their input domains inside the cyto- Thisprototypicdomainorganizationcanbevariedbyinclu-
plasm(Fig.1C).Thisclassofsensorproteinsdetectsthepres- sion of “linker” regions, such as the HAMP or PAS domain
enceofcytoplasmicsolutesorofproteinssignalingthemeta- (12, 276), between TMR2 and the transmitter domain or by
bolic or developmental state of the cell or of the cell cycle. additionalphosphorylationdomainsdownstreamofthetrans-
OthercytoplasmicTCSrespondtodiffusibleorinternalstimuli, mitter domain (Fig. 2). The linker domains vary considerably
suchasO orH ,orstimulitransmittedbyTMsensors. in size, extent, and type. The additional phosphorylation do-
2 2
VOL.70,2006 STIMULUS PERCEPTION IN SIGNAL-TRANSDUCING HKs 913
TABLE 1. Names,termdefinitions,andfeaturesofconservedsignalingandsensorydomains
Characteristics,conserved
Domaina Nameorigin Localization Size(aa) Reference(s)
features,and/orremarks
Signaltransduction
domains
HAMP FoundinHK,adenylylcyclase, Cytoplasmic (cid:3)50 2(cid:4)-helices(coiled-coilstructure); 12,276
methyl-carrierprotein, importantlinkerdomainfor
phosphatase signaltransductionfrom
periplasmicinputto
cytoplasmickinasedomain;
littlesequenceconservation
HATPase_c Histidinekinase-typeATPase Cytoplasmic (cid:3)140 CatalyticdomainofHK; 87,279,280
catalyticdomain phosphoryltransferfromATP
toHisKAdomain;harborsthe
conservedN,D,F,andG
boxes
HisKA/DHp HistidinekinaseAdomain Cytoplasmic (cid:3)80 Dimerizationand 87,279,280
dimerization/Hisphosphotransfer phosphoacceptordomainof D
HK;harborstheHboxwith o
theinvarianthistidineresidue, w
thesiteofautophosphorylation n
inHK lo
HPt Histidinephosphotransfer Cytoplasmic (cid:3)100 PresentattheNterminusin 169 a
proteinswhichundergo d
autophosphorylation;contains e
d
anactivehistidineresiduethat

mediatesthephosphotransfer fr
reactions o
MA Methyl-acceptingchemotaxis Cytoplasmic (cid:3)260 Undergoesreversiblemethylation 27,195,222 m
domain (atspecificGluresidues)in h
responsetoattractantsor t
t
repellantsduringbacterial p
chemotaxis;interactswith :/
/
CheA-likeHKsandCheW m
REC Receiverdomain Cytoplasmic (cid:3)100 N-terminalreceiverdomainofa 200 m
responseregulator;containsa
b
phosphoacceptorsite(an r
invariantaspartateresidue) .a
thatisphosphorylatedbyHK s
proteins m
.
o
Sensoryinput r
domains g
5TMR-LYT 5TMreceptordomain,LytS-like Intramembrane (cid:3)90 Inputdomainwith5TMRfound 5 o/
inLytS-YhcKtypeHKs;little n
sequenceconservation
7TMR-DISM 7TMreceptorswithdiverse Intramembrane (cid:3)200 Inputdomainwith7TMR;little 5 A
p
intracellularsignalingmodules sequenceconservation r
CACHE FoundinCa2(cid:1)channelsand Periplasmic (cid:3)80 Implicatedinsmall-molecule 6 il
chemotaxisreceptors binding 4
CHASE-CHASE6 Cyclase/Hiskinase-associated Periplasmic 150–300 Sixindividualgroupsof 7,288 ,
2
sensingextracellular conservedputativeperiplasmic- 0
sensingdomains;predictedto 1
sensediversestimulisuchas 9
aminoacids,peptides, b
cytokines,andturgor y
DISMED2 DISMextracellulardomain2 Periplasmic (cid:3)130 Putativecarbohydrate-binding 5 g
domainattheNterminiof u
most7TMR-DISMsensor e
kinases;predictedtoadoptan s
all-(cid:5)-foldwithajellyroll t
topology
GAF FoundincGMPphosphodiesterase, Cytoplasmic (cid:3)150 Oneofthelargestfamiliesof 13
adenylylcyclase,FhlA small-moleculebindingunits;
PAS-likefold;predictedto
bindcyclicnucleotides,suchas
cGMP/cAMP
KdpD DomainfoundinKdpD-likeHKs Cytoplasmic (cid:3)210 Sensordomainofosmosensitive 267
K(cid:1)channelHKs;possiblythe
inputdomainresponsiblefor
sensingturgorpressure
MASE1 Membrane-associatedsensor Intramembrane (cid:3)280 8-TMRintegral-membrane 5,186
domain1 domain,withconserved
residues(3Pro,3Trp
intrahelical);stimuliunknown;
alternativename,8TMR-UT
Continuedonfollowingpage
914 MASCHER ET AL. MICROBIOL.MOL.BIOL.REV.
TABLE 1—Continued
Characteristics,conserved
Domaina Nameorigin Localization Size(aa) Reference(s)
features,and/orremarks
MCP Methyl-acceptingchemotaxis Transmembrane 500–600 TMsensorproteinsconsistingof 239,244,278
protein aperiplasmicinputdomain
(CACHE,PAS,GAF,or
TarH)andusuallytwo
cytoplasmicdomains(HAMP
andMA)
MHYT ConservedMet,His,Tyr,andThr Intramembrane (cid:3)190 6TMRwithshortlinkers; 67
residues characteristicintrahelical
MH(YT)motifinTMR2,
TMR4,andTMR6;implicated
inbindingmetals(e.g.,copper)
PAS InitiallyidentifiedinthePER, Cytoplasmic (cid:3)110 Conservedandwidelydistributed 254,289
ARNT,andSIMproteins redoxsensordomain;binds
heme,flavin,andadenineand
senseslightandoxygen(among D
others);oftenoccurs o
duplicatedand/ortogetherwith w
aC-terminalextension(PAC n
domain) lo
PBPb Periplasmicsolute-bindingproteins, Periplasmic (cid:3)220 Thoughttodirectlybind 252 a
bacterial substrate(aminoacidsor d
opines)closetotheinner e
d
membrane;typicalfeatureof

BvgS-likeHKs;oftenoccurs fr
duplicated o
Phytochrome Sensorofbacteriophytochromes Cytoplasmic (cid:3)180 Photochromicphotoreceptors 135,265 m
thatemployabilin-type h
chromophoretoactasa t
t
red/far-red-regulatedreversible p
photoreceptor;bindlinear :/
/
tetrapyrroles m
Reg_prop Regulatorypropeller Periplasmic (cid:3)600 14tandemrepeatsof14aaeach 63 m
form27-bladed(cid:5)-propellers
SS(S)F Sodium/solutesymporterfamily Intramembrane (cid:3)400 13TMR;catalyzetheuptakeofa 124,125 br
widevarietyofsolutes .a
(includingsugars,proline,and s
iodide)bysodiummotiveforce m
TarH Tar-homologousdomain Periplasmic (cid:3)150 Ligand-bindingdomainsof 172 .
o
chemotaxisreceptors(MCP); r
bindahugevarietyoflow- g
molecular-weightsolutessuch /
o
asaminoacids,sugars(as n
attractants),andmetalions(as
A
repellents)
USP Universalstressproteinfamily Cytoplasmic (cid:3)130 OccurinKdpD-likeHKs; 152,236 p
r
conserved(cid:4)/(cid:5)-fold;function il
unclear(ATPbinding?) 4
,

aNamesofdomainsderivedfromtheSMARTorPfamdatabase. 2
0
1
9

mainscomprisereceiverdomainstypicalforRRs,withacon- conserveddomains(5–7,67,68,186,203,288)arefoundalsoin b
y
served Asp residue for phosphorylation and an additional othersignalingandsensingsystems.Thefunctionsofonlyalim-
g
transmitter (histidine-containing phosphotransfer [HPt]) do- itednumberofsuchsensingdomainsofHKshasbeenelucidated, u
e
main(Fig.2).“Hybrid”kinasesofthistypeconstituteaphos- in particular those of periplasmic (CitA, DcuS, and PhoQ) and s
t
phorelay, predominantly in gram-negative bacteria (285), cytoplasmic(FixL)PASdomains(40,79,85,137,144,201,219).
whereasphosphorelaysystemsofgram-positivebacteria,such Othersaredefinedonlybymeansofsequenceconservation(such
astheregulatorycascadeofsporulationinitiationinB.subtilis astheCHASEdomains),andtheirfunctionsandstimuliremain
(58), normally consist of individual proteins mediating the tobeidentified(65).Additionally,manyHKs,includingparadig-
stepwisephosphotransfer. matic HKs such as EnvZ, do not contain conserved features in
Sensor kinases sharing the prototypical architecture form a theirperiplasmicdomains.Correspondingtothediversityofsen-
large and highly diverse group with regard to composition and sorydomains,manydifferentmechanismsofstimulusperception
function of the sensory or input domain (Fig. 3). The HKs are and processing can be anticipated, although these are mostly
grouped primarily based on features of the periplasmic sensing unknown.Thereare,however,afewwellcharacterizedexamples
domains,toreflectfunctionalandsensoryprinciples.Thelinker thatcanserveasmodels.
domainwillbeusedinspecificcasesasanadditionalcriterionfor Perhaps the simplest mechanism for signal detection by
subgrouping,whereastransmitterdomainswillnotbeconsidered. periplasmic-sensingHKsoccursbydirectinteractionbetweenthe
Despiteagreatdiversityinsequenceandstimulusspecificity, sensordomainandachemicallydefinedsmallmolecule,suchas
theinputdomainsofmanysensorscanbegroupedbysequence nitrate/nitriteforNarXorcitrateforCitA(115,242).Forsomeof
alignment into a few families (Fig. 3 and Table 2). Most of the theperiplasmic-sensingHKs,thebindingsiteandstructureofthe
VOL.70,2006 STIMULUS PERCEPTION IN SIGNAL-TRANSDUCING HKs 915
D
o
w
n
lo
a
d
e
d

f
r
o
m

h
t
t
p
:
/
/
m
m
b
r
.
a
s
FIG. 3. Domainarchitectureofperiplasmic-sensinghistidinekinases.ThefigureisbasedonthegraphicaloutputoftheSMARTwebinterface m
athttp://smart.embl-heidelberg.de(229),withmodifications.Thescalebarisinaminoacids.Blueverticalbarsrepresentputativetransmembrane .o
helices.Sizesandpositionsofconserveddomainsareindicatedbythelabeledsymbols.Notethatthetransmitterdomainsaresimplified,andas r
g
adefault,onlytheHisKAandHATPase_cdomainsareshown.Additionalcytoplasmicdomainsarepossibleandwidespreadbutwereignoredin /

allbutobligatorycases(i.e.,PASdomainforCitA-likeHKsandHAMPdomainforNarXQ-likeHKs).AdiagonalbarattheCterminusofthe o
n
transmitter domain indicates the possible occurrence of hybrid kinases in that subgroup of sensor kinases. The periplasmic PAS domain of

CitA/DcuS (in parentheses) is conserved by three-dimensional structure only and not by sequence. It is therefore not detectable by sequence A
p
analysis.VanS/PrmB-likeproteinsaredescribedinthe“Intramembrane-SensingHKs:CellEnvelopeStressSensorswithTwoTMR(LiaS/BceS-
r
LikeHKs)”section.Seethetextfordetails. il
4
,

2
0
periplasmicbindingdomainhasbeendetermined(seebelow).In linkerregions.Thesequencesoftheextracytoplasmicregions 1
othercases,chemicalstimuliaresensedindirectlythroughinter- of most prototypical periplasmic-sensing HKs reveal no con- 9

actionwithaperiplasmicsolute-bindingprotein,suchasglucose served or known sensing domains. Structural analysis of the by
by the sugar-binding protein ChvE for interaction with the PhoQ periplasmic domain revealed, however, a PAS domain, g
Agrobacterium tumefaciens VirA sensor kinase (234). Alterna- whichwasnotrecognizedbysequenceanalysis(similartothe ue
tively,signalingmaybetriggeredbymechanical,electrochemical, PAS domains of CitA and DcuS [40]). The other classes of s
t
or concentration gradient stimuli, resulting in a conformational periplasmic-sensingHKsarecharacterizedbythepresenceof
changeoftheinputdomain,ashasbeenhypothesizedforosmo-
definedtypesofsensorydomainsintheperiplasmandbythe
larityorturgorsensors.Thereisalsogrowingevidencethatother
presenceofextendedlinkerdomains.EnvZ,PhoQ,TorS,and
periplasmic-sensingTCSuseadditionalproteins,whichtransmita
VirAareimportantmembersoftheprototypicalHKsandwill
primarysignaltotheHK,therebycomplicatingtheidentification
bediscussedinmoredetail.
oftheprimarystimulus.FormostTCStheexacttypeofstimulus
EnvZ,togetherwithitscognateRROmpR,playsacentral
isnotknown.Inthefollowingdescriptions,wewillconcentrateon
role in the adaptation of E. coli to changes in extracellular
characterizing general properties of the families, which will be
osmolarity.EnvZisoneofthebest-understoodHKs,andstud-
exemplifiedbyafewprominentmembers.
iesofthisproteinhavecontributedenormouslytoourunder-
standing of dimerization and phosphorylation reactions in
PrototypicalPeriplasmic-SensingHistidineKinases
membrane-boundHKs.Thestructuresofthetransmittersub-
Prototypical periplasmic-sensing histidine kinases are com- domains were solved by nuclear magnetic resonance (253,
posedoftwoTMheliceswithaninterveningextracytoplasmic 257).TheHisKAorDHpsubdomainconsistsoftwo(cid:4)helices
domainof50to300aminoacids(aa),lackinglargecytoplasmic thatdimerizetoformafour-helixbundle,whichrepresentsthe
916 MASCHER ET AL. MICROBIOL.MOL.BIOL.REV.
TABLE 2. Groupsofbacterialhistidinekinasesaccordingtothedomainarchitecturesoftheirsensingdomains
Transmembraneregion Cytoplasmicregion
(Nterminal) (Cterminal)
No.of
Histidinekinasegroup Bacterialgroupf Reference(s)
kinasese
Length
Architecturea Architecturec HKclassd
(aa)b
Periplasmicsensing (cid:3)2,500
Prototypicalsensors TMR-(50–300aa)- 100–350 (HAMP)- NAg (cid:6)1,000 NA 18,40,139,
TMR HK-(REC-HPt) 284
NarX/Q-likeh TMR-P-60aa-P(cid:7)- (cid:3)180 HAMP-Y(Cys)Q- HPK7 30 Proteobacteria 35,242
TMR HK
CitA/DcuS-like TMR-“PAS”-TMR (cid:3)200 PAS-HK HPK5 20 Proteobacteria 144,201,219
VirA-like TMR-200aa-TMR (cid:3)300 HK-REC HPK4 20 Agrobacterium 36,234,235
VanS-like TMR-(25–30aa)- (cid:3)90 HK HPK1a 10–20 Actinobacteria 104,106
TMR
PrmB-like TMR-(30–40aa)- (cid:3)90 HAMP-HK HPK2a 10–20 Proteobacteria 281
TMR D
o
PBPbsensors TMR-PBPb - 300–600 (PAS-PAC)-HK- HPK1b 50 Proteobacteria 26,148,252 w
(BvgS-like) TMR 1–3 (REC-HPt) n
CACHEsensors TMR-100-CACHE- (cid:3)300 HK NAi 3 NAi 6 lo
a
50-TMR d
CHASE-CHASE6 TMR-CHASE-TMR (cid:3)380 (HAMP)-(PAS- HPK1a/b 100j NAj 7,288 e
sensors 1/3 PAC)-HK d
Reg-propsensors TMR-2(cid:5)prop- (cid:3)1,000 HK-REC-AraC- HPK1a 40 Bacteroides 63 fr
o
(YYY)-TMR HTH
m

h
TMRassociated (cid:3)800 tt
LiaS-like TMR-(5–25aa)- (cid:3)70 (HAMP)-HK HPK7 20 Firmicutes 120,151,166, p:
TMR 167 //
m
BceS-like TMR-(5–10aa)- (cid:3)60 HK HPK3i 70 Firmicutes 166,167,194
m
TMR
DesK-like 4/5TMR (cid:3)150 HK HPK7 20 Firmicutes 3 b
r
RegB-like 3TMR-RB-3TMR (cid:3)200 HKcys HPK3e 30 Proteobacteria 55 .a
ComD/AgrC-like 6/7TMR (cid:3)210 HK HPK10 30 Firmicutes 98,119, s
m
160–162
ComP-like 8/10TMR 300–350 HK HPK7 10 Firmicutes 208 .o
LuxN-like 8/10TMR (cid:3)300 HK-REC HPK4 10 Vibrio 62 rg
PutP/CbrA-like 12–20TMR 400–600 (PAS)-HK HPK3d 30 Proteobacteria 124,125 /

(SSSFcontaining) o
MHYTsensors 6TMR (cid:3)300 HK-(REC-Hpt) NAi 3 NAi 67 n
UhpB-like MASE1 (cid:3)300 HK HPK7 20 Proteobacteria 130 A
p
MASEsensors MASE1 250–400 (PAS-PAC)-HK- HPK1b 10 Proteobacteria 5,186 r
REC il
7TMR-DISM-like TMR-(DISMED2)- (cid:3)200/400 HK-(REC) HPK1b 30 Proteobacteria/ 5 4
,
7TMR spirochetes 2
LytS-like 6TMR(TMR- (cid:3)200 GAF-HK HPK8 40 Firmicutes/ 5 0
1
5TMR-LYT) proteobacteria
9

b
y
Cytoplasmicsensingk (cid:3)1,600 65,88
KdpD-like KdpD-Usp-4TMR (cid:3)500 GAF-HK HPK1a 100 Firmicutes/ 267 gu
(membrane- proteobacteria e
anchored,N- s
t
terminalinput)
ArcB-like TMR-(10–20aa)- (cid:3)80 Leucinezipper- HPK1b 20 Proteobacteria 163
(membrane TMR PAS-HK-REC-
anchored,C- Hpt
terminalinput)
FixL-like 2/3TMRm (cid:3)100m PAS-PAC-(PAS- HPK4 30 Proteobacteria 77,79
(membrane- PAC)-HK
anchored,C-
terminalinput)
CheA-like(soluble) HPT-HK-CheW HPK9 150 Proteobacteria 243,244,250,
278
Phytochrome PAS-GAF- HPK3h 20 133,135,265
sensorsl(soluble) phytochrome-HK
Continuedonfollowingpage
VOL.70,2006 STIMULUS PERCEPTION IN SIGNAL-TRANSDUCING HKs 917
TABLE 2—Continued
aConserveddomainswereidentifiedusingtheSMARTtool(229).Sizesareaveragesandcanvarygreatly.TMRareputative.RB,RegBbox;P/P(cid:7),boxesdefined
byStewart(242);2(cid:5)-prop,twoseven-bladedsensor-specific(cid:5)-propellers,basedonthepresenceof14Reg_propdomains(Pfamentry),arrangedintandemrepeats.
AllotherdomainsareasdefinedintheoriginalpublicationsortheSMART,Interpro,orPfamdatabaseentries(seethetextandreferencestherein).
bAveragesizeoftheinputdomain,includingall(flanking)transmembraneregions.
cConserveddomainswereidentifiedusingtheSMARTtool(229).HK,histidinekinase(consistingoftheSMARTHisKAandHATPase_cdomains);HKcys,
histidinekinasedomainbearingadditionalconserved(redox-active)cysteineresidues;REC,receiverdomain.Allotherdomainsareaccordingtodatabaseentriesor
previouspublications(seethetextandreferences).
dAssignmentisderivedfrommultiple-sequencealignmentsofeachgroup,basedonthehistidinekinaseclassificationsystemofGrebeandStock(87).
eDuetothedynamicsintheavailabilityofsequenceinformationinthedatabases,thenumbersgivenshouldbeviewedasroughestimates,indicativeonlyofthe
distributionandgeneralimportanceofeachgroupofsensorkinases.
fPredominantbacterialgroupsaregivenonlyif(cid:6)70%ofthecorrespondingsequencesarederivedfromonephylum.
gNA,notapplicable.
hAccordingtoStewart(242),NarX-andNarQ-likesensorsdifferintheabsenceorpresenceofthecysteine-richcentraldomain,respectively.
iNAduetothesmallnumberofHKscontainingthesedomains.
jCHASEtoCHASE6domain-containingsensorsformsixindependentsubgroups,belongingtodifferentHKclassesfromdifferentgroupsoforganisms.Therefore,
nodetailscanbegivenforthesekinasesasawhole.
kOftheextremelydiversegroupofcytoplasmic-sensingHKs,onlyindividualprominentexamplesarerepresentedinthistable.Seethetextfordetails.Thereare D
(cid:3)1,200solublekinases. o
lThereare110additionalphytochromesensorsinplants. w
mAnumberofFixL-likekinasesaresolubleproteins,lackingtheTMR. n
lo
a
d
e
coreofthetransmitterdomain(53,257).Thephospho-accept- PhoQPTCSregulatesmodificationoflipidAandotherviru- d
ingHisresidueprotrudesfromthehelicesandisaccessibleto lence factors, including those for antimicrobial peptide resis- f
r
phosphorylation from the surface by the C-terminal catalytic tance(61,91,174,217). o
m
HATPasesubdomain.Thus,EnvZisafunctionaldimer,with ThesensorkinasePhoQisactivatedatlowconcentrationsof
boththecytoplasmictransmitterandtheperiplasmicdomains cations,suchasMg2(cid:1),andbyincreasingconcentrationsofthe ht
t
contributing to dimerization. The structures of the HisKA/ antimicrobialpeptides(i.e.,duringinvasionofmacrophagesby p
:
/
DHpandHATPasedomainsgaveimportantinsightsintothe the bacteria) but is repressed by high concentrations of diva- /
m
functionsoftheindividualdomains.Recently,thestructureof lentcations(70).Thus,theseeffectorshaveopposingeffectson m
theentirecytoplasmictransmitter,includingtheHAMPlinker PhoQfunction(Fig.4).Thecrystalstructureoftheperiplasmic b
domain, of an HK was solved (165), which will help us to PhoQ domain was determined in the Ca2(cid:1) bound state (40). r.
a
understandhowthesignalfromTMhelix2isreceivedbythe The periplasmic domain belongs to the PAS domain family, s
m
cytoplasmicdomainandtransferredtothekinasedomain. despiteanapparentlackofsequencesimilaritytoPASdomain
.
Despite the wealth of knowledge gained over the years on proteins. The structure matches that of CitA and DcuS (see o
r
thefunctionofthisarchetypicalTCS,littleisknownaboutthe below), but there is an insertion of two (cid:4)-helices in the PAS g
/

mechanismofosmosensingbyEnvZ.Aclosehomolog,EnvZ fold. This insertion creates a flat and negatively charged sur- o
n
of Xenorhabdus nematophilus, completely lacks a periplasmic faceononesideoftheprotein,whichisderivedfromGluand
A
domain [see “Intramembrane-Sensing HKs: Cell Envelope Asp residues. Unlike the PAS domains of DcuS and CitA, p
StressSensorswithTwoTMR(LiaS/BceS-LikeHKs)”]butis thePhoQperiplasmicdomaincontainsnocavityordiscrete ril
stillabletocomplementanE.colienvZnullmutant(251).In binding pocket for ligand binding. It is proposed that bind- 4
E. coli EnvZ, partial deletions of the periplasmic domain, or ing of the antimicrobial peptides and Mg2(cid:1) occurs at the , 2
even a complete replacement with the periplasmic region of acidicsurfaceatthemembrane-proximalsideoftheprotein, 0
1
the nonhomologous PhoR of B. subtilis, did not significantly whichisinclosecontacttothelipidsurfaceofthecytoplas- 9

altertheprocessofosmosensing(156).Theseresultscallinto mic membrane (Fig. 4A). The acidic surface binds at least b
y
questionadirectandessentialroleoftheperiplasmicdomain threeMg2(cid:1)ions,whichareproposedtoformcationbridges
g
ofE.coliEnvZinosmosensing.Workontheyeastosmosensor betweentheacidicregionofPhoQandtheacidicmembrane u
e
Sln1 suggests that these kinases sense turgor as the key input phospholipids (40) (Fig. 4A). s
t
stimulus. A systematic deletion/replacement analysis of the IonicinteractionstethertheperiplasmicdomainofPhoQ
periplasmicdomainofSln1suggeststhatonlytheintegrityof to the membrane. In this state, the kinase domain of PhoQ
theperiplasmicdomainasawholeisnecessaryforosmosens- isinactive(18,40).Thebindingofantimicrobialpeptidesis
ing,ratherthanspecificaminoacidssequenceorregions(220). suggestedtodisplacethecationsandtodisrupttheinterac-
Thisworkcomplementsandsupportstheresultsobtainedfor tion between PhoQ and the membrane. The antimicrobial
E.coliEnvZ. peptides are suggested to function as a lever (Fig. 4B),
ThePhoQ/PhoPTCSisimportantforthecontrolofpatho- liftingtheperiplasmicdomainoffthemembrane.Thestruc-
genesis of Salmonella and other gram-negative bacteria. Mul- tural distortion could be transmitted mechanically to the
ticellularorganismsinhibitinvadingbacteriabyuseofcationic TM helices, with a resultant motion of the TM helices,
antimicrobialpeptides,whichcontainapositivenetchargeand resulting in the autophosphorylation of PhoQ. Thus, the
an amphipathic structure for interaction with negatively stimuli of PhoQ (antimicrobial peptides and divalent cat-
charged biological membranes (43). The bacteria acquire re- ions)arenotboundatadistinctbindingpocketbutfunction
sistance to the antimicrobial peptides by modifying the cell by resolving and forming interactions between PhoQ and
surface,inparticularlipopolysaccharideandlipidA,whichare the membrane surface (18).
modified in antimicrobial peptide-resistant strains (174). The Otherprototypicperiplasmic-sensingHKs,i.e.,VirA,TorS,
918 MASCHER ET AL. MICROBIOL.MOL.BIOL.REV.
D
o
w
n
lo
a
d
e
d

f
r
o
m

h
t
t
p
:
/
/
FIG. 4. Structure of the periplasmic input domain of PhoQ and model for the sensing mechanism of cations and antimicrobial peptides. m
(A)Thecrystalstructureandchargeprofileofthesurfacefacingtheoutersideofthecytoplasmicmembraneareshownontheleft.Theresidues m
importantforcoordinatingthedivalentmetalionsareshown.ThecrystalstructureofthedimericPhoQsensordomain(upperpanel)formsaflat b
r
surfacethatcomesinclosecontacttothemembrane.Thebottompartofthisdomaincontainsahighlynegativelychargedsurfacethatparticipates .
a
in metal binding (lower panel, view from the membrane). Red represents negatively charged residues. NT, N terminus; CT, C terminus. s
(B)WorkingmodelforthecompetitivebindingofMg2(cid:1)andcationicantimicrobialpeptidestoPhoQ.Divalentcations,suchasCa2(cid:1)orMg2(cid:1) m
(shownasgreenballs),bindtotheacidicsurface(red)andrepressPhoQactivitybylockingthePhoQsensordomaininaninactiveconformation .
o
(top panel). Cationic antimicrobial peptides interact with membrane phospholipids, thereby coming in close contact with the Ca2(cid:1) and Mg2(cid:1) r
g
bindingsitesofPhoQ.TheycompetewithanddisplacedivalentcationsfromPhoQ(middlepanel).Thisprovokesaconformationalchangeofthe /

inputdomain,whichleadstoautophosphorylationofthetransmitterdomainandtherebyactivationofPhoQ(lowerpanel).Seethetextfordetails. o
(Reprintedfromreference18withpermissionfromElsevier.) n

A
p
r
il
and BctE, sense stimuli by interaction of their periplasmic expression of the torCAD operon, encoding the periplasmic tri- 4
,
domainswithotherproteinsinthesamecompartment.These methylamine-N-oxide(TMAO)reductase(TorA),aTorA-spe- 2
proteins are often solute-binding proteins, which are part of cificchaperone(TorD),andthec-typecytochromeTorC(171). 0
1
binding-protein-dependenttransportsystems.Periplasmicsol- TorCisamembrane-boundproteinandcarriesthecatalyticdo- 9

ute-binding proteins are also used for sensing by methyl-ac- maincontainingpentahemecontheperiplasmicsurfaceofthe b
y
cepting chemotaxis proteins (MCP) in bacterial chemotaxis membrane.TorCinteractswiththecatalyticdomainofTorAin
g
(147,252). the periplasm and forms a functional TorC-TorA respiratory u
e
Expressionofvirulence(vir)genesinthegram-negativeplant complexofTMAOreductase(83).TorSdetectsTMAOpresum- s
t
pathogen Agrobacterium tumefaciens is regulated by the VirAG ablybyitsperiplasmicregion(123)andstimulatestheexpression
TCSinresponsetoacidicpH.ThedecreaseinpHiscausedby ofthetorCADoperon.Inaddition,apoTorClackingthehemeC
phenolic compounds (such as acetosyringone) that are released groupsbindstothesensorTorSandnegativelyregulateskinase
by wounded plant cells (reviewed in references 99 and 287). In activity (i.e., when it is inactive and not able to form an active
addition,aldosemonosaccharides(e.g.,arabinose)exudedfrom TorC-TorArespiratorycomplex).Thisdirectprotein-proteinin-
wounded plant sites serve as strong enhancers of phenolic-in- teractioninvolvestheC-terminalpartofTorCandtheperiplas-
ducedHKactivity(34,235).Thesugarissensedbybindingtothe micdomainofTorS(83).
periplasmicsugar-bindingproteinChvE,whichinturninteracts Bordetella pertussis uses the BctDE TCS for controlling the
withthe220-aa-longperiplasmicinputdomainofVirA(36,234). expressionofacitrateuptakesystemduringgrowthoncitrate
Direct sensing of phenolic compounds by VirA occurs in the (9).Thecitratecarrierisatripartitetricarboxylatetransporter,
cytoplasmic linker region between TMR2 and the HisKA do- consistingoftheBctABmembranecarrierproteins.BctCisan
main,i.e.,atasitedifferentfromthatofChvEinteraction(20,36, extracytoplasmic citrate-binding protein and represents the
49, 204, 277). Recently, it was established that the periplasmic third component of the tripartite tricarboxylate transporter
domainisalsoinvolvedinpHsensing(69). system. BctE is a prototypical HK with two TM helices and
TheTorS/TorRtwo-componentsystemofE.colicontrolsthe requires BctC for response to the citrate. Citrate-liganded
VOL.70,2006 STIMULUS PERCEPTION IN SIGNAL-TRANSDUCING HKs 919
BctC interacts with the periplasmic sensing domain of BctE
andcontrolsthefunctionalstateofthesensor.
NarX/NarQ-LikeSensorsofEnvironmental
NitrateandNitrite
A second, well-characterized group of periplasmic-sensing
HKs is represented by the NarX-NarQ-like sensors, which
contain defined “boxes” or domains in the periplasm and ex-
tended linker domains between TMR2 and the transmitter
domain(Fig.3).Inproteobacteria,anaerobicrespiratorygene
expressioniscontrolledbyoneoftwonitratereductase(Nar)
TCS, NarXL or NarQP, in response to environmental nitrate
and nitrite. E. coli and Salmonella enterica contain both
paralogs.Theconcentrationofthetworespiratoryoxidantsis
D
sensed through ligand binding by the periplasmic domain
o
(length, 115 aa) of the two corresponding HKs, NarX and w
NarQ. Multiple sequence alignments reveal two conserved n
stretches of 18 amino acid residues in length that flank each lo
a
periplasmicsideofthetwoTMhelices(PandP(cid:7)boxes)(Fig. d
e
3)(242).Alaninesubstitutionsofhighlyconservedresiduesin d
thePbox(butnotinP(cid:7))stronglyaffectedsignaldetectionand f
r
wereabletorenderNarXandNarQinaconstitutivelyactive o
m
(“locked-on”)orinactive(“locked-off”)form(35,242,275).In
h
additiontotheconservedextracellularboxes,bothtypesofNar t
t
sensors have an extended cytoplasmic linker region. In the p
:
/
linker region, “locked-on” mutations that are dominant over /
m
“locked-off” mutations in the P box were identified (35, 131). m
Therefore, it was proposed that signal processing requires ni- b
r
trate (or nitrite) detection in the periplasm by the P box, .
a
followed by signal transfer across the membrane and to the s
m
kinase,withthelatterdependingontransmissionbythelinker
.
region.ThelinkerregionconsistsofaHAMPdomain(12)and o
r
anunusual“Y-Cys-Q”moduleinfrontoftheHisKAdomain. FIG. 5. Structures of the periplasmic sensing domains of DcuS g
/
Similarly to other HAMP linkers, the sequence immediately (A)andCitA(B).ThestructuresfortheperiplasmicdomainsofCitA o
andDcuSarederivedfromhttp://www.rcsb.org.Theresiduesrequired n
followsTMR2andispredictedtoformtwoshortamphipathic forC-dicarboxylatesensingbyDcuS(144,201)anddirectbindingof A
(cid:4)-helices,whicharejoinedbyanunstructuredconnector.Mu- citrate4 toCitA(75,219)areshown.Thecorrespondingsitesarehigh- p
tationsintheHAMPlinkerdisturbthefunctionofNarXand lightedinthestructure. ril
NarQ,anditwasconcludedthattheHAMPlinkerisrequired 4
,
forpropersignaltransduction(10,11).Thecentral“Y-Cys-Q” 2
moduleconsistsofthreeparts:(i)theYbox,aleucine-zipper ulategenesencodingcarriersandenzymesforthedegradation 0
1
like domain of 32 amino acids in length; (ii) the central cys- ofexternallysuppliedcitrateorC -dicarboxylates,inparticular 9
4
teine cluster, which is present in NarX but missing in NarQ- under anaerobic growth conditions. Metabolism of endog- b
y
like HKs; and (iii) the Q linker, which is reminiscent of glu- enouslyproducedcitrateorC -dicarboxylatesisnotregulated
4 g
tamine-rich flexible interdomain linkers (Fig. 3) (242). While byCitA/DcuS.Inbindingstudies,theperiplasmicdomainsof u
e
deletionandalaninereplacementmutagenesiscouldestablish CitA of Klebsiella pneumoniae and E. coli function as high- s
t
a role of the Y box and Q linker in intramolecular signal affinity citrate receptors with K values in the micromolar
D
transduction, no phenotype was observed in mutants lacking range(136).Themolecularinteractionsbetweenthesensordo-
oneormoreoftheconservedcysteineresiduesofthecentral main and its ligand have been elucidated through the cocrystal
region(242).TheresponseregulatorNarLisamemberofthe structure of the periplasmic domain of CitA of K. pneumoniae
FixJ/LuxRfamilyandisstructurallyandfunctionallywellchar- and mutagenesis (Fig. 5) (75, 137, 219). The structure of the
acterized (19). Taken together, the NarXQ-like HKs are dis- correspondingdomainoftheC -dicarboxylatesensorDcuSofE.
4
tinctfrommostotherperiplasmic-sensingkinasesduetocon- coli was determined in solution by nuclear magnetic resonance
servedperiplasmicandcytoplasmicdomainsinvolvedinsignal (Fig. 5) (201). The extracellular input domains of both sensors
detectionandtransduction. adoptaPAS-likefoldwithacorestructureconsistingoffouror
five(cid:5)-strands,whichisflankedbythreeN-terminal(cid:4)-helicesand
CitrateandC4-DicarboxylateSensorProteins one C-terminal (cid:4)-helix. There is only one small (cid:4)-helix located
CitAandDcuS withinthe(cid:5)-strands(201).Theneareststructuralneighboristhe
CitA/DcuS-likeHKsrespondtotheenvironmentalconcen- PAS domain of the photoactive yellow protein from Halorho-
trations of citrate (CitA) or C -dicarboxylates and citrate dospirahalophila(28),whichhasasimilartertiarystructurebut
4
(DcuS)and,togetherwiththeircognateRRsCitB/DcuR,reg- shows no obvious sequence similarity. The (cid:5)-strand structure