Review Article Archaea Signal Recognition Particle Shows the Way

12 Pages·2014·1.54 MB·English

HindawiPublishingCorporation
Archaea
Volume2010,ArticleID485051,11pages
doi:10.1155/2010/485051
Review Article
Archaea Signal Recognition Particle Shows the Way
ChristianZwieb1andShakhawatBhuiyan2
1DepartmentofMolecularBiology,UniversityofTexasHealthScienceCenteratTyler,11937USHighway271,Tyler,
TX75708-3154,USA
2DepartmentofBiology,DivisionofBusinessandSciences,JarvisChristianCollege,P.O.Box1470,Hawkins,TX75765,USA
CorrespondenceshouldbeaddressedtoChristianZwieb,[email protected]
Received15April2010;Accepted14May2010
AcademicEditor:JerryEichler
Copyright©2010C.ZwiebandS.Bhuiyan.ThisisanopenaccessarticledistributedundertheCreativeCommonsAttribution
License,whichpermitsunrestricteduse,distribution,andreproductioninanymedium,providedtheoriginalworkisproperly
cited.
ArchaeaSRPiscomposedofanSRPRNAmoleculeandtwoboundproteinsnamedSRP19andSRP54.Regulatedbythebinding
andhydrolysisofguanosinetriphosphates,theRNA-boundSRP54proteintransientlyassociatesnotonlywiththehydrophobic
signalsequenceasitemergesfromtheribosomalexittunnel,butalsointeractswiththemembrane-associatedSRPreceptor(FtsY).
ComparativeanalysesofthearchaeagenomesandtheirSRPcomponentsequences,combinedwithstructuralandbiochemical
data,supportaprominentroleoftheSRPRNAintheassemblyandfunctionofthearchaeaSRP.The5emotif,whichineukaryotes
bindsa72kilodaltonprotein,ispreservedinmostarchaeaSRPRNAsdespitethelackofanarchaeaSRP72homolog.Theprimary
functionofthe5eregionmaybetoserveasahinge,strategicallypositionedbetweenthesmallandlargeSRPdomain,allowing
theelongatedSRPtobindsimultaneouslytodistantribosomalsites.SRP19,requiredineukaryotesforinitiatingSRPassembly,
appearstoplayasubordinateroleinthearchaeaSRPormaybedefunct.TheN-terminalAregionandanovelC-terminalRregion
ofthearchaeaSRPreceptor(FtsY)arestrikinglydiverseorabsentevenamongthemembersofataxonomicsubgroup.
1.Introduction the SRP delays or blocks the translation of the to-be-
targeted polypeptides. Translation resumes when the SRP-
Protein sorting fundamentally maintains the identity and bound ribosome nascent chain complex (RNC) binds to
function of every cell with participation of the signal the membrane-associated FtsY (filamentous temperature
recognition particle (SRP). SRP components have been sensitive Y) or, in eukaryotes, the alpha subunit of the
found in nearly all organisms [1]. Except in chloroplasts, SRP receptor (SRα). The interaction between SRP54 and
SRP is a ribonucleoprotein [2]. The SRP RNA is typically the SR increases the affinity of the proteins for guanosine
composed of about 300 nucleotide residues and forms a triphosphate, promotes the release of the signal from the
complex with an extraordinarily conserved protein named SRP, and interjects the signal sequence of the nascent
SRP54inarchaeaandeukaryaorFfh(fifty-fourhomolog)in polypeptide into the protein-conducting channel (PCC) of
thebacteria.A19kDaprotein,SRP19,ispresentinarchaea thecellmembrane.Translationandproteintranslocationor
andeukarya,butabsentinthebacteria.Polypeptideswhich membrane insertion take place during ongoing translation
are homologous to the eukaryal SRP9/14 and SRP68/72 (cotranslationaltranslocation),and,uponhydrolysisoftwo
heterodimers have not been found in the archaea genome GTP molecules, the SRP returns to its free cytosolic state
sequencesgivingrisetoanarchaeaSRPwhichisdominated ready to initiate another protein targeting cycle (Figure 1)
byRNA[3,4]. [5–9].
SRPinteractswithsecretorysignalormembrane-anchor Eventhougharchaeamembranesdiffersignificantlyfrom
sequences upon their emergence from the ribosomal exit the cell membranes of eukaryotes and bacteria with regard
tunnel. In vitro and in vivo experiments carried out totheuseofglycerol-etherlipidsandisoprenoidsidechains
in eukaryotic protein sorting systems have shown that [10,11],noobviousadaptationsforsurvivalunderextreme
2 Archaea
S-layer 4
Membrane PCC N
2GTP
?
E PA
FtsY
2GDP+2Pi
SRP E PA
5(cid:2) 3(cid:2)
E PA 5(cid:2) 3(cid:2)
3
N
E PA 5(cid:2) 3(cid:2)
2
5(cid:2) 3(cid:2) Cytoplasm
Ribosome 1
Figure1:HypotheticalstepsintheSRP-mediatedtargetingofarchaeaproteins.Step1:Aribosome(gray,withA,PandEtRNAbinding
sites)inthecytoplasmtranslatesamRNAmolecule(black,5(cid:2)and3(cid:2)endsareindicated)whichencodesaN-terminalsignalormembrane-
anchorsequence(blackdots).Step2:Asthesignalemergesfromthelargeribosomalsubunit,itisrecognizedbytheelongatedSRPand
furthertranslationmaybehalted.Step3:TheSRP-boundribosomenascentchaincomplex(RNC)bindstofreeormembrane-associated
FtsY(arrow).Step4:AfterGTPhydrolysis,SRPhasbeenreleased,translationresumes,andthetargetedproteinisthreadedthroughthe
protein-conducting channel (PCC). The surface (S) layer, present in most archaea, is anchored to a glycerol-ether lipids-containing cell
membrane.
conditionsareapparentintheSRPcomponents.Likebacte- archaeaaswellascertainbacteria(e.g.,BacilliandClostridia)
ria,archaeacontainonlyoneSRPreceptorpolypeptide,FtsY, pairtheirterminalregionstoformahelix1.Helix7hasbeen
ahomologoftheeukaryalSRαsubunit.Thesignalsequences foundonlyineukaryalSRPRNAswhereitismostprominent
ofthearchaeaandbacteriaareinterchangeable[12,13],and insomefungiandprotozoans[1].
archaeasignalpeptidaseswhichremovethesignalsequence Using the previously described sequence identification
afterproteintranslocationhavebeenidentified[14].Archaea procedures and covariation rules (see Methods) we aligned
lack homologs of the bacterial and eukaryal translocation 81archaeaSRPRNAsequencesandarrangedthemaccording
ATPases SecA and Kar2p/BiP. They possess, however, Sec61 to NCBI’s taxonomy [35]. The shared alignment pairing
(the PCC) and a Tat translocase system [15]. These SRP maskallowstodeducephylogeneticallysupportedSRPRNA
independent means of protein delivery have been discussed secondarystructuresforeachofthealignedsequences.With
recently[16,17]andwillnotbereviewedhere. afewexceptions,asequencecorrespondstoaknownspecies.
Solving the structures of numerous archaea SRP com- The apical loops of SRP RNA helices 3 and 4 form a
ponents and their complexes at high resolution (Table 1) tertiary interaction which is well supported by covarying
has been crucial for understanding the intricacy of protein compensatory base changes. The UGUNR sequence motif
targetinginallorganisms.Withinthisstructuralframework, (N is A, C, G or U, R is a purine) located between these
the increasing number of newly identified archaea genome helices(labeledUGUinFigure2(a))ispartofastructurally
sequences provides an opportunity to review and discover important U-turn. Both features promote the high degree
not only archaea-specific SRP features, but also draw phy- of compactness of the small SRP domain. It remains to be
logenic distinctions which may pave the way for a better determined how similar the structure of the protein-free
understandingofthefunctionandevolutionofeverySRP. small domain of the archaea SRP is to the solved crystal
structureofthemammalianAludomainincomplexwiththe
2.ArchaealSRPRNA SRP9/14proteinheterodimer[36].
As previously noted and confirmed by mining of the
Unlike the bacterial and eukaryal SRP RNAs, their archaea largercollectionofarchaeaSRPRNAsequences,deviations
counterparts vary little in shape and size (approximately fromtheUGUNRmotifoccurinseveralgroups[37].Con-
300nucleotideresidues).Thismaybeduetorelativelyslow spicuouserosionsofthesmalldomaintakeplaceintheSRP
evolutionary rates as has been observed previously when RNAs of several Desulfurococcales and in Nitrosopumilus
the relative conservation of archaea protein sequences was maritimus SCM1. Base pairs which typically participate in
investigated [31]. Archaea SRP RNA secondary structures theformationofhelices1and3areabsentinthesesequences,
possessextensivelybasepairedregionswhichformapromi- whileotherresiduesperhapsformanextendedhelix4.Due
nentcentralhelixflankedbyasmall(orAlu)andalarge(or totherelativelysmallnumberofavailablesequenceswithin
S)domain(Figure2(a)).Thus,theyresemblethesecondary thesesubgroupsitisnotyetpossibletoconclusivelyproveor
structuresofthemammalianSRPRNAs.Heliceshavebeen disproveplausiblebasepairs.
assignednumbersfromonetoeight,andhelicalsectionare Another hydrogen-bonded tertiary interaction engages
designatedwithlettersatof[32,33].TheSRPRNAsofmost twoadenosineswithintheapicaltetraloopsofhelices6and8
Archaea 3
Table1:High-resolutionstructuresofarchaealSRPcomponents.Indicatedarethearchaeasubdomains(CrenarchaeotaorEuryarchaeota),
speciesnames,components,andmethods(X-RaydiffractionofNMR)usedforstructuredetermination.ThepdbIDsalloweasyretrieval
ofthecoordinates[18].Theprotein-conductingchannelisabbreviatedasPCC.AdditionalnonarchaeaSRPhigh-resolutionstructuresare
listedathttp://rnp.uthct.edu/rnp/SRPDB/srpstructures.html.
Subdomains Species Components Methods pdb References
Crenarchaeota Acidianusambivalens SRP54NG X-Ray 1J8M,1J8Y [19]
Sulfolobussolfactaricus SRP54withhelix8 X-Ray 1QZW [20]
SRP54dimer X-Ray 1QZX [20]
SRP54withsignalpeptide X-Ray 3KL4 [21]
SRP19withhelix6andhelix8 X-Ray 3KTV,3KTW [22]
Euryarchaeota Archaeoglobusfulgidus SRP19 NMR 1KVN,1KVV [23]
SRP54M NMR 2JQE [24]
Methanococcusjannaschii SRP19withSRP54withRNA X-Ray 2V3C [25]
SRP19withhelix6andhelix8 X-Ray 1LNG [26]
Helix6andhelix8 X-Ray 1Z43 [27]
PCC X-Ray 1RHZ,1RH5 [28]
Pyrococcusfuriosus SRP19 X-Ray 3DLU,3DLV,3DM5 [29]
SRP54 X-Ray 3DLU,3DLV,3DM5 [29]
FtsY X-Ray 3E70,3DM9,3DMD [30]
Table2:TaxonomicdistributionofarchaeaSRPfeatures.Indicatedarethearchaeasubdomains,thenumberofspeciesidentifiedineach
group,andarepresentativespecies.FeaturesaretheUGUNRmotif(NisanynucleotideandRisapurineresidue),helices(typically1to
4)inthesmallSRPdomain(SD),theGNARtetranucleotideloop(tetraloop)ofhelix6,theGGAAtetraloopofhelix8,proteinsSRP19
and SRP54 (SRP19/54), and the acidic (A) domain of the FtsY receptor (FtsY-A). “+” shows presence, “−” absence, and “±” indicates
that this feature is present only in a subset of the group members. Sequences deviating from the top-listed motif (e.g., the GGGA in
theThermoproteales)aregiven.Thestructuralalignmentsofthe81identifiedarchaeaSRPRNAsandtheproteinalignmentsofSRP19,
SRP54andFtsYareprovidedonlineaslistedinSupplementaryMaterials2availableonlineatdoi:10.1155/2010/485051andareavailableat
http://rnp.uthct.edu/rnp/SRPDB/srprna.html.FeaturesoftheSRPRNAinallthreedomainsoflifehavebeenrecentlydescribedindetailin
[1].
Subdomains Groups(n) PrototypicalSpecies UGUNR SDhelices GNAR GGAA SRP19/54 FtsY-A
some
Crenarchaeota Desulfurococcales(5) Pyrodictiumoccultum − + + + −
absent
Sulfolobales(12) Sulfolobussolfataricus ± + + + + +,varies
Thermoproteus
Thermoproteales(4) − + + GGGA + −
neutrophilusV24Sta
Euryarchaeota Archaeoglobales(2) Archaeoglobusfulgidus + + + + + ±
Halobacteriumspecies ±,some
Halobacteriales(10) − + + + +
NRC-1 long
Methanobacterium +,some
Methanobacteriales(3) + + + + +
thermoautotrophicum long
Methanocaldococcus
Methanococcales(12) + + varies + + ±
jannaschiiDSM2661
Methanomicrobiales Methanoculleus
UAUAA + + + + ±
(1) marisnigriJR1
Methanosarcina
Methanosarcinales(5) + + + + + ±
acetivorans
Methanopyruskandleri
Methanopyrales(1) + + + GAGA + −
AV19
Pyrococcushorikoshii ±,some
Thermococcales(14) + + + + +
OT3 long
Thermoplasma
Thermoplasmatales(3) − + AAAG + + −
acidophilum
Candidatus CandidatusKorarchaeum
Korarchaeota − + + + + −
Korarchaeum(1) cryptofilumOPF8
Nitrosopumilus some
Thaumarchaeota Nitrosopumilales(1) − + GGGA + −
maritimusSCM1 absent
4 Archaea
GNAR GA
T-loop GC GG160
motif C G
C G
G C
Archaeoglobus fulgidus SRP RNA U U
C G
150 G U 6
G C
G C
CCGCCGAU50 CCG GC170
Tertiary interaction UmGotUif 434300UAAAGAAUCCCCUGCGCCCG GCCGGG GGGGGGUUGGCGA22CG010GC60GCAUCGG GAGU5AGUGCGG(cid:2)C5CGCC3Aa0GCCC0A3G17(cid:2)GA301CG0CGCGAGGA2CG9UG0GCGC80AUCGGGU5bA CA AAUG28GC0CGCG9CG0GCCG5CGcGCAAA2CG7UC0UGACG10GU0GUGCGC5UAdCG26CG0GCUAhGC1i1GCn0AGgGCeAGG AGUAGC25GC1052G Ue0GC mCGGUUo5G etGCGifGC24GC0CGCGUA1U3CG0GGCG5GC2fGC30CGS1CG4AR0GC82PCGa2A05GGUAUUGG4CC CCAAUCCAUAUUAGCCGGGGGGG1GC810AA90 Tertiary interaction
binding G C
G C
motif A+C 8b
C+A
210 G+G
A+G
G C
G C 200
G C
A G
Small (Alu) domain Large (S) domain AG
(a)
Consensus Sulfolobales Thermoproteales Eukaryota
GN - - C C GC - - C C GU- - C C GN- - C C
C N GG C N GG C N GG C N GG
NNN NCU CCG NNA
Archaeoglobales Halobacteriales Methanobacteriales
Protein
GU- - C C GU- -C C GU- - C C SRP72
C G GG C G GG C A R G
UGG CUR A YU
Methanococcales Methanosarcinales Thermococcales Desulfurococcales Thermoplasmata Korarchaeota
GU- - C C GU- - Y C GU--C C GY- -C C GU- -C C GU- -C C
C G GG C A R G C A R G C N GG C G GG C G GG
NNG YYR NNG N3-4 NN NN
(b) (c)
Figure2:ArchaeaSRPRNAfeatures.(a)SecondarystructureofArchaeoglobusfulgidusSRPRNA.(b)Consensus-matching5emotifssorted
bytheirtaxonomicmembership.(c)Mismatching5emotifs.Helicesarenumberedfrom1to8andhelicalsectionsarelabeledwithlettersa
tof[33].Forexample,helix1iscomposedofresiduesonetosevenwhicharebasepairedwithresidues303to310;helix2consistsofresidues
atpositionstento13basepairedwiththeresiduesatpositions59to62.Theextendedhelix5containssixhelicalsections,5ato5f.Helix7is
lackingintheSRPRNAsofthearchaea.The5(cid:2)-and3(cid:2)-endsareshown,andresiduesarelabeledinten-residueincrements.Basepairswere
determinedbycomparativesequenceanalysis[32]andbyconsideringhigh-resolutiondata(Table1).Theapproximateextentsofthelarge
(S)andthesmall(Alu)domainsareindicated.ShownindarkgrayaretheUGUNRmotif(labeledUGU)inthesmalldomain,the5emotif
withinhelicalsection5eattheindicatedhinge[34],theGNARapicaltetraloopofhelix6andtheSRP54bindingmotifofhelix8inthelarge
domain.Dashedlinessuggesttertiaryinteractions.
(A159andA205inArchaeoglobusfulgidus,Figure2(a)).This and likely exists in all archaea and eukaryotic SRP RNAs.
long-rangeinteractionwasfirstseeninthecrystalstructures The participating adenosine of helix 6 is presented within
ofMethanococcusjannaschiiSRPRNAfromthelargedomain a GNAR tetranucleotide loop (tetraloop) in most archaea
(Table 1). The adenosine clamp severely constraints the SRPRNAs,butdeviates(AAAG)fromtheconsensusinthe
arrangement of helices 6 and 8. It is highly conserved four SRP RNA sequences of the Thermoplasmatales. The
Archaea 5
interacting helix 8 has a GRRA loop with GGAA being the Such an interpretation is supported by the finding that 5e
mostfrequentlyrepresentedtetranucleotide.GGGAisfound ispresentinSRPRNAswithastandardsetofhelicesintheir
intheThermoprotealesandThaumarchaeota(Nitrosopumi- smallSRPdomain[38].Conversely,Figure2(c)andthedata
lales), and GAGA in the Methanopyrales. These helix 8 shown in Table 2 suggest that SRP RNAs deviate from the
tetraloopsequencesareprobablyusefulwhenattemptingto 5econsensuswhentheylacktheUGUNRmotiforwhenthe
identifyandclassifythearchaeaSRPRNAs(Table2). smallSRPdomainiseroded.Thesehinge-impairedarchaea
SRPRNAsmayfunctioninamodewhichresemblestheSRP-
mediatedproteintargetingofthemajorityofbacteriawhich
3.The5eMotif:ACaseforMolecular lackthesmallSRPdomain.
Exaptation
The11-nucleotide5eelementisthemostrecentlydiscovered 4.ProteinSRP19,IsItRequired?
SRP RNA motif and has been helpful in the prediction of
SRP RNA genes [38]. The motif consists of four base pairs AlthoughproteinSRP19wasthoughttobeabsentincertain
interruptedbyathree-nucleotideloop.Twoofthebasepairs archaea genomes [3], its genes (91 sequences) have now
are symmetrically arranged G-C pairs. The comparison of been identified in all archaea subgroups (Table 2). SRP19
141 eukaryal and 28 archaea sequences shows that the first coexist with SRP RNA helix 6 as part of the large SRP
residue of the eukaryotic 5e loop is a conserved adenosine domain. Mainly due to the reduced size of its loop 4,
(A240 in human SRP RNA) in the eukarya (Figure 2(b)) the archaea SRP19 is generally somewhat shorter than its
[39]. In the archaea, the corresponding nucleotide can be eukaryotichomolog(Figure3,top,graytriangle).TheNMR
anyresidue,andonlytwohalobacterialsequences(Haloferax structureofArchaeoglobusfulgidushasbeensolved[23],and
volcanii,GenBankAccessionAF395888,andHalomicrobium severalcrystalstructuresofthefreeandRNA-boundSRP19
mukohataei, GenBank Accession CP001688) possess an have been determined (Table 1) revealing a single-domain
adenosine. compactlyfoldedprotein.
Systematic site-directed mutagenesis of the 5e region Certain conserved amino acid residues (Y/W and GR
showed that human SRP RNA with a single A240G change in loop 1; Figure 3, top) participate in the binding to the
wasunabletoformacomplexwithfull-lengthhumanSRP72 SRP RNA through induced fit mechanisms involving both
[39]. The 5e RNA was found to bind a 56 amino acid- the protein and the RNA. For example, loop 3 (Figure 3,
residue polypeptide of human SRP72 which contained the top) of Archaeoglobus fulgidus SRP19 reorders and adopts
consensussequencePDPXRWLPXXER(Xisforanyamino a single conformation upon binding to RNA [23]. In the
acid residue) [40]. Bioinformatic analyses identified two Thermococcales, loop 3 is enlarged and disordered and,
relativelypoorconsensussequencematchesinthegenomes uponbinding,rearrangestoassistintheproperfoldingofthe
of archaea, one with a methyl coenzyme M reductase of SRP RNA [29]. This mechanism of mutual conformational
an uncultured methanogenic archaeon (GenBank Acces- adjustmenthasbeenobservedinseveralotherprotein-RNA
sion ABI18429), the other with a hypothetical protein of complexes[44].
Pyrobaculum islandicum DSM 4184 (GenBank Accession Ineukaryoticcells,SRPisassembledinthenucleolusand
ABL88435). These relationships are likely coincidental and, transported to the cytosol where it associates with SRP54
untilprovenotherwise,areconsistentwiththenotionthata [45, 46]. Archaea SRPs contain only two proteins, SRP19
functional equivalent of the eukaryotic SRP72 is lacking in and SRP54, and assemble in the cytosol. The mammalian
thearchaea. SRP19 is required to position SRP RNA helices 6 and 8 in
Theconservedadenosineinthe5emotifoftheeukaryal, a side-by-side fashion and expose the SRP54 binding site
butnotthearchaealSRPRNAssuggeststhatthe5eelement through a conformational collapse in helix 8. In contrast,
was recruited in evolution to supply a new function to the archaea SRP RNA binds SRP54 even in the absence of
protein-rich eukaryotic SRP thereby providing a striking SRP19[47,48].RNasesusceptibilitymeasurementsofwild-
exampleformolecularexaptation,definedastheutilization type and mutant Archaeoglobus fulgidus SRP RNAs show
of a feature for a function which differs from what it was that the conserved adenosine of the GNAR tetraloop in
originally developed for [41, 42]. Because human SRP72 helix 6, and not SRP19, is responsible for a compactly
binds strongly to the Haloferax volcanii SRP RNA [40], the arranged large SRP domain [49]. Indeed, helices 6 and
structures of the 5e region of archaea and eukaryotes are 8 are closely packed in the protein-free crystal structures
apparentlyverysimilar. of Methanococcus jannaschii and Sulfolobus solfataricus SRP
The 5e RNA fragment is remarkably resistant towards RNAs[22,27].
ribonucleolytic attack [39] indicating that it is compactly Figure 4 indicates that helix 6 and helix 8 interact with
folded and may resemble the structure of an RNA kink- eachothernotonlythroughtheirdistaltetraloopadenosines
turn [43]. Although 5e conforms only loosely to the K- but also via internal looped-out residues. However, the
turnconsensussecondarystructure,3Dmolecularmodeling asymmetric internal loop of helix 8 engages in distinctly
demonstrates compatible structures (Zwieb, unpublished). different ways. In the human SRP RNA, two adenosines
Thissuggestthat5eispartofthebendorhingewhichallows protrude from the short strand of the asymmetric loop to
theelongatedSRPtoadjusttothecurvatureoftheribosome form A-minor motifs with helix 6 [50]. In contrast, in the
and bind simultaneously to separate ribosomal sites [34]. MethanococcusjannaschiiRNAstructures,twoadenosinesof
6 Archaea
SRP19 Thermococcales Eukarya
insert insert
Y L1 L2 L3 L4
W
GR
N C
1 20 40 60 80 100 120 140
Helix6 Helix8
Halobacteriales
Thermococcales insert
Sulfolobales insert GLMD Methanococcales
insert LEKEV insert
SRP54 I-box GY RXLGXGD GG
FL
N G M
N C
1 50 100 150 200 250 300 350 400 450
FtsY-NG Signal Helix8
Unculturedmarine
crenarchaeotarepeats
Nitrosopumilus EPVP
FtsY I-box maritimusrepeats
EPTP
DV P GKTT GR GG
A N G R
N C
1 250 300 350 400 450 500 550 600 800
SRP54-NG
Figure3:FeaturesofSRP19(top),SRP54(center)andtheFtsYSRPreceptor(bottom).IndicatedaretheN-andC-termini.Helicesare
shownascylinders,beta-sheetsasarrows,andsomeloopsarelabeledwithanarchandtheletterL.Invariantorhighlyconservedresidues
areshownboxed,andseveralaminoacidresidueinsertswhicharecharacteristicfortheindicatedtaxonomicgroupsareshownasbold
letters.NumberingisaccordingtothecolumnpositionsofeachproteinalignmentaccessibleaslistedinSupplementaryMaterials2and
attheSRPdatabaseathttp://rnp.uthct.edu/rnp/SRPDB/SRPDB.html).RegionsandsiteswhichinteractwithotherSRPcomponentsorthe
signalsequencearemarkedwithbracketsbeloweachpanel.
helix 6 are bulged out and interact in the minor groove of 5.SRP54
helix8[25].
Deletion of the yeast SRP19 homolog Sec65 was shown SRP54,oritsbacterialhomologFfh,ispresentinallorgan-
to be lethal to the eukaryote Yarrowia lipolytica [51]. In isms,includingthechloroplastSRPswhichlackanSRPRNA
the archaea, structural and biochemical data as well as the [2].DeletionoftheHaloferaxvolcaniiSRP54generesultsin
deviation from the GNAR tetraloop motif observed within thelossofcellviabilityasproofofthecentralroleofSRP54
the Thermoplasmatales (Table 2) suggest that SRP19 is in archaea protein targeting [52, 53]. Sequence and three-
not required for SRP assembly and dispensable for protein dimensional structure (Table 1) of the protein are highly
sorting and survival. In fact, deletion of SRP19 from the conserved. These properties are readily explained by the
Haloferaxvolcaniigenomehadnoeffectonproteintranslo- numerous interactions which engage SRP54 in the binding
cationormembraneinsertion.Increasedlevelsofmembrane not only to the SRP RNA, but also the signal sequence
bacterioruberin were detected in the deletion mutant and andtheFtsYSRPreceptor.Theobservedexceptionallyhigh
significant amounts of SRP19 mRNA were observed in level of conservation likely reflects the need to carry out
nonmutatedcells[52]suggestingarelativelyminorpossibly multiple binding reactions in a coordinated dynamically
regulatory function for SRP19. Although the protein might GTP-regulated way to ensure proper and efficient delivery
participateinamoresubstantivewaywhenHaloferaxvolcanii ofawidevarietyofsignalsequence-taggedproteinsintothe
is challenged to survive in external environments, the data PCC.
demonstrate the diminished importance of the archaea The functions of SRP54 are brought about by three
SRP19whencomparedtoitssignificantroleforthesurvival domains. The N-terminal (N) domain is composed of
ofeukaryoticcells. a bundle of four alpha helices, the GTPase (G) domain
Archaea 7
Membrane exceptional conservation of SRP54 throughout all domains
A R oflifesuggeststhatarchaeaemployasimilarifnotidentical
N G
FtsY signalrecognitionmechanism.TheNGregioncanbeinclose
N proximity to SRP RNA helix 8 and, in archaea, appears to
G
engagealsohelix6[25].
SRP54
Signal The alignment of 103 archaea SRP54 sequences reveals
M
several group-specific amino acid residue insertions, for
19 8 example a GY in the G domain of Sulfolobales which
6 might modulate the GTPase activity. Into the M domain,
ThermococcalesinsertthesequenceLEKEV,Halobacteriales
GLMD, and Methanococcales GG (Figure 3). These amino
acidresidueshavethepotentialtocontributetothebinding
Figure 4: Interactions between the components of archaea SRP-
oftheproteintotheSRPRNA,tosignalpeptiderecognition
mediated protein targeting. Schematic drawing of the coaxially-
or other yet to be specified enhanced functions. Regardless
arranged SRP RNA helices 6 and 8 bound together by SRP19
oftheirpotentialsignificance,theseshortpeptidesequences
and two tertiary interactions (dashed lines). The M-domain of
are useful for assigning SRP54 sequences to their proper
the SRP54 protein (dark gray) binds to SRP RNA helix 8 as well
as the signal sequence (black). The NG-domains of SRP54 and taxonomicgroup.
theFtsYSRPreceptorarearrangedquasisymmetricallyandpoised
to separate upon the hydrolysis of two G-domain-bound GTP
molecules.TheN-terminalregionlabeledA(foracidic)andtheC- 6.FtsY:TheSRPReceptor
terminalrepeatregion(R)ofFtsYarevariableormaybeabsent(see
Table2). The SRP receptor (SR) of the eukarya is composed of
the peripheral membrane SRα and the integral membrane
SRβ proteins. Bacteria and archaea possess only FtsY, a
contains a unique insertion (I-box) which serves as a homolog of SRα [60]. Sequence comparisons of FtsY with
guanine nucleotide-exchange factors (GEFs) and stabilizes SRP54 suggest a gene duplication event [61] and support
the nucleotide free protein [54, 55], and the methionine- the classification into the three domains of life as well as
rich (M) domain binds to the SRP RNA and the signal thecloserootingofarchaeaandeukarya[62].ArchaeaFtsY
sequence(Figure3,center).Thepredominantlyalphahelical sharesitsconservedNGregionwithNGofSRP54,including
M domain contains an extended segment (the so-called the I-box, but differs from SRP54 with respect to several
fingerloop) which delineates or is folded into a groove short amino acid stretches as revealed by the alignment of
which accepts signal sequences [20, 21, 56]. This wide 95archaeaFtsYsequences(Figure3,SupplementaryMaterial
and short hydrophobic groove was observed also in the 1). The NG regions are symmetrically arranged in three
crystal structure of the RNA-bound Escherichia coli Ffh dimensions to constitute the structural and functional core
[57]. The NMR structure of the Archaeoglobus fulgidus of signal sequence release and nascent polypeptide delivery
SRP54 M domain [24] is similar to these crystal structures intothecellmembrane(Figure4)bymutuallycatalyzingthe
and disfavors another proposed mode whereby the signal hydrolysisofGTP[63–65].
sequencebindswithinalongandnarrowgrooveofSRP54M As has been observed within the bacterial genomes
[28, 50]. The conformations of the fingerloop in solution [66, 67] several archaea FtsY sequences consist only of the
suggest that it adaptively binds and stabilizes the signal NG domain and lack an N-terminal acidic (A) domain.
sequences.Bindingisweak[24]andlikelyreversibleinorder Diversity with respect to the A domain is observed even
topermitsignalsequencereleaseuponthebindingofSRP54 within a single archaea subgroup (Table 2). Full-length
to the SRP receptor. The molecular details of the contacts HaloferaxvolcaniiFtsYaswellaspolypeptideslackingtheA
made by a signal peptide with the Sulfolobus solfataricus domain were shown to bind to inverted membrane vesicles
SRP54havebeenrevealedrecentlyandsuggestthatportions indicating that the A domain is dispensable for attaching
of the fingerloop may adopt an alpha helical conformation FtsY to the membrane. Instead, the A domain may play
[21]. a role in recruiting SRP to the haloarchaeal membrane
Adding to the intricacy of signal sequence recognition, [68, 69]. Assuming a pool of free FtsY in the cytosol
the M domain and the NG region of SRP54 are joined [70, 71] (Figure 1) these findings are particularly relevant.
together via a flexible linker. This region has the consensus On the other hand, fluorescence microscopy showed that
sequence RXLGXGD and allows the RNA-bound SRP54 to almostalloftheEscherichiacoliFtsYassociatesinvivowith
undergosubstantialstructuralrearrangementsuponbinding the inner membrane, and any soluble FtsY is unlikely to
toasignalsequence[20,22].Consistentwiththisassertion, contributetoproteintargeting[72].AlthougharchaeaFtsY
site-directed mutagenesis experiments of mammalian SRP might interact with the membrane in similar manners as
[58] and a recent crosslinking study of the Escherichia has been observed in bacteria and chloroplast [2, 73–76],
coli SRP [59] demonstrate the involvement of the signal themoleculardetailsofthebindingcouldbequitedifferent
sequence not only with the M domain, but also the NG given the differences in membrane lipid composition. FtsY
region. No evidence for the binding of NG to signal might also interact directly with a cytosolically exposed
sequences has been provided in the archaea. However, the portion of the PCC [77, 78]. In either case, one would
8 Archaea
expectfunctionalsynchronicitybetweenGTPhydrolysisand theconserved5emotifanditsrelationshiptoaflexiblehinge
deliveryofproteinintothePCC[79]. or a bend in the elongated SRP? It will also be important
IntheFtsYsequencesoftheunculturedmarineCrenar- to further elucidate the role of the archaea FtsY, its role in
chaeota we discovered a C-terminal proline-rich extension, thecytosolaswellasthemolecularfeatureswhichpromote
named R for its motif repetitions (see Figures 3 and 4). its association with archaea membranes. As in the past, the
Up to 12 EPVP repeats (accession numbers ABZ10052, studiesofthearchaeaSRPareexpectedtocontributeinmany
ABZ08863, ABZ09152, ABZ09615) and five EPVV repeats ways to our grasp of SRP-mediated protein targeting in all
(ABZ098531)werepresentintheRregion.Similarmultiple organism.
repeats with the sequence EPTP were seen also in the FtsY
oftheThaumarchaeotumNitrosopumilusmaritimusSCM1.
9.Methods
Details of the R-regions can be inspected in an updated
archaealFtsYalignmentprovidedattheSRPDB[37].Aswith
Sets of representative sequences were used as input to Perl
much of our limited understanding of the role of FtsY in
scripts written to identify sequence homologs in the NCBI
thearchaea,itremainstobedeterminediftheserepeatsare
databases[90].RNAsequenceswerealignedsemiautomati-
expressedandhaveafunctioninproteinexport.
callywithSARSE[91];proteinsequenceswerealignedusing
MUSCLE [92] followed by manual adjustments in Jalview
7.ArchaeaSRPFunctionandEvolution [93]. The alignments are available through the links listed
inSupplementaryMaterial2.Inaddition,theSRPdatabase
During the past years, several interesting puzzle pieces providestablesofalphabeticallyandphylogeneticallysorted
with respect to SRP-mediated protein translocation and sequencesathttp://rnp.uthct.edu/rnp/SRPDB/SRPDB.html.
membrane insertion in the archaea have been assembled.
TheSRPsoftheCrenarchaeotumAcidianusambivalensand
Acknowledgments
theEuryarchaeotaArchaeoglobusfulgidus,Pyrococcusfuriosus
and Haloferax volcanii have been reconstituted [47, 48, 80–
TheauthorsaregratefultotheAmericanHeartAssociation,
82], and the ability of an archaea SRP54 to participate in SouthCentralAffiliate,forsupport(no.09GRNT2080038).
signal sequence recognition has been demonstrated [81].
S.Bhuiyan is supported by a UNIMET grant from the
Nevertheless, the role of SRP within the archaeal cell is
National Aeronautics and Space Administration and the
stillpoorlyunderstood.Examplesofbothproteinsynthesis-
United Negro College Fund Special Programs Corporation
linked (cotranslational) and posttranslational translocation
NASA Science and Technology Institute for Minority Insti-
have been provided [83–87], but to what degree these
tutionProjectNNA06CB14H.
findingsarerepresentativeremainstobeinvestigatedfurther
[16].
The proposal that signal sequences might interact with References
the SRP RNA has fed the imagination that the primitive
[1] M. A. Rosenblad, N. Larsen, T. Samuelsson, and C. Zwieb,
SRPwascomposedonlyofRNA[57,88].However,because
“KinshipintheSRPRNAfamily,”RNABiology,vol.6,no.5,
of the proteinaceous nature of the signal, a scenario in
pp.508–516,2009.
whichSRPRNAcoemergedwithevolutionaryprecursorsof
[2] K. F. Stengel, I. Holdermann, P. Cain, C. Robinson, K.
SRP54/Ffh/FtsYappearstobemoreplausible.Furthermore,
Wild, and I. Sinning, “Structural basis for specific substrate
the recent structure of the signal peptide-bound Sulfolobus recognition by the chloroplast signal recognition particle
solfataricusSRP54(Ffh)showsthatthesignalpeptideistoo protein cpSRP43,” Science, vol. 321, no. 5886, pp. 253–256,
farremovedfromtheSRPRNAtomakedirectcontact[21]. 2008.
If the small (Alu) SRP domain was a feature of the [3] C.ZwiebandJ.Eichler,“Gettingontarget:thearchaealsignal
primitive SRP which subsequently was lost in evolutionary recognitionparticle,”Archaea,vol.1,no.1,pp.27–34,2002.
time;themajorityofthebacteriaismoredifficulttodiscern. [4] R. G. Moll, “The archaeal signal recognition particle: steps
Asanotherpossibilityarchaeaandcertainbacteriamayhave toward membrane binding,” Journal of Bioenergetics and
Biomembranes,vol.36,no.1,pp.47–53,2004.
been faced independently with the need to enlarge a small
[5] H. G. Koch, M. Moser, and M. Mu¨ller, “Signal recogni-
primitive SRP, maybe to slow down translation rates and
tion particle-dependent protein targeting, universal to all
provide more time for ensuring the delivery of proteins to
kingdoms of life,” Reviews of Physiology, Biochemistry and
themembraneashasbeenobservedineukarya[89].
Pharmacology,vol.146,pp.55–94,2003.
[6] K. Nagai, C. Oubridge, A. Kuglstatter, E. Menichelli, C. Isel,
andL.Jovine,“Structure,functionandevolutionofthesignal
8.FutureDirections
recognitionparticle,”EMBOJournal,vol.22,no.14,pp.3479–
3485,2003.
With respect to the RNA-rich archaea SRP it would be
[7] J. A. Doudna and R. T. Batey, “Structural insights into the
desirabletobetterunderstandthestructureandfunctionof
signal recognition particle,” Annual Review of Biochemistry,
the protein-free small SRP domain. For example, what, in
vol.73,pp.539–557,2004.
moleculardetail,allowsthesmalldomaintofoldbackonto [8] M.HalicandR.Beckmann,“Thesignalrecognitionparticle
helix5inordertoapproximatetheshapeanddimensionsof anditsinteractionsduringproteintargeting,”CurrentOpinion
theeukaryalSRP[36]?Whatisthefunctionalsignificanceof inStructuralBiology,vol.15,no.1,pp.116–125,2005.
Archaea 9
[9] S.-O.ShanandP.Walter,“Co-translationalproteintargeting [26] T. Hainzl, S. Huang, and A. E. Sauer-Eriksson, “Structure
bythesignalrecognitionparticle,”FEBSLetters,vol.579,no. of the SRP19-RNA complex and implications for signal
4,pp.921–926,2005. recognitionparticleassembly,”Nature,vol.417,no.6890,pp.
[10] G.D.Sprott,“Structuresofarchaebacterialmembranelipids,” 767–771,2002.
JournalofBioenergeticsandBiomembranes,vol.24,no.6,pp. [27] T. Hainzl, S. Huang, and A. E. Sauer-Eriksson, “Structural
555–566,1992. insights into SRP RNA: an induced fit mechanism for SRP
[11] J.L.C.M.VandeVossenberg,A.J.M.Driessen,andW.N. assembly,”RNA,vol.11,no.7,pp.1043–1050,2005.
Konings,“Theessenceofbeingextremophilic:theroleofthe [28] W. M. Clemons Jr., K. Gowda, S. D. Black, C. Zwieb,
uniquearchaealmembranelipids,”Extremophiles,vol.2,no. and V. Ramakrishnan, “Crystal structure of the conserved
3,pp.163–170,1998. subdomain of human protein SRP54M at 2.1 A˚ resolution:
[12] G. von Heijne, “The signal peptide,” Journal of Membrane evidenceforthemechanismofsignalpeptidebinding,”Journal
Biology,vol.115,no.3,pp.195–201,1990. ofMolecularBiology,vol.292,no.3,pp.697–705,1999.
[29] P. F. Egea, J. Napetschnig, P. Walter, and R. M. Stroud,
[13] M. Pohlschro¨der, M. I. Gime´nez, and K. F. Jarrell, “Protein
“Structures of SRP54 and SRP19, the two proteins that
transport in Archaea: Sec and twin arginine translocation
organizetheribonucleiccoreofthesignalrecognitionparticle
pathways,”CurrentOpinioninMicrobiology,vol.8,no.6,pp.
fromPyrococcusfuriosus,”PLoSOne,vol.3,no.10,ArticleID
713–719,2005.
e3528,2008.
[14] S. Y. M. Ng, B. Chaban, D. J. VanDyke, and K. F. Jarrell,
[30] P.F.Egea,H.Tsuruta,G.P.deLeon,J.Napetschnig,P.Walter,
“Archaealsignalpeptidases,”Microbiology,vol.153,no.2,pp.
andR.M.Stroud,“Structuresofthesignalrecognitionparticle
305–314,2007.
receptorfromtheArchaeonPyrococcusfuriosus:Implications
[15] S.-V.Albers,Z.Szabo´,andA.J.M.Driessen,“Proteinsecretion
forthetargetingstepatthemembrane,”PLoSOne,vol.3,no.
intheArchaea:multiplepathstowardsauniquecellsurface,”
11,ArticleIDe3619,2008.
NatureReviewsMicrobiology,vol.4,no.7,pp.537–547,2006.
[31] J.M.KollmanandR.F.Doolittle,“Determiningtherelative
[16] D.CaloandJ.Eichler,“CrossingthemembraneinArchaea,the
ratesofchangeforprokaryoticandeukaryoticproteinswith
thirddomainoflife,”BiochimicaetBiophysicaActa.Inpress.
ancientlyduplicatedparalogs,”JournalofMolecularEvolution,
[17] J.Yuan,J.C.Zweers,J.M.vanDijl,andR.E.Dalbey,“Protein vol.51,no.2,pp.173–181,2000.
transport across and into cell membranes in bacteria and
[32] N.LarsenandC.Zwieb,“SRP-RNAsequencealignmentand
archaea,” Cellular and Molecular Life Sciences, vol. 67, no. 2,
secondarystructure,”NucleicAcidsResearch,vol.19,no.2,pp.
pp.179–199,2010.
209–215,1991.
[18] A. Kouranov, L. Xie, J. de la Cruz et al., “The RCSB PDB [33] C. Zwieb, R. W. Van Nues, M. A. Rosenblad, J. D. Brown,
information portal for structural genomics,” Nucleic Acids andT.Samuelsson,“Anomenclatureforallsignalrecognition
Research,vol.34,pp.D302–305,2006. particleRNAs,”RNA,vol.11,no.1,pp.7–13,2005.
[19] G. Montoya, K. te Kaat, R. Moll, G. Scha¨fer, and I. Sinning, [34] M.Halic,T.Becker,M.R.Pooletal.,“Structureofthesignal
“ThecrystalstructureoftheconservedGTPaseofSRP54from recognition particle interacting with the elongation-arrested
the archaeon Acidianus ambivalens and its comparison with ribosome,”Nature,vol.427,no.6977,pp.808–814,2004.
relatedstructuressuggestsamodelfortheSRP-SRPreceptor [35] D. A. Benson, I. Karsch-Mizrachi, D. J. Lipman, J. Ostell,
complex,”Structure,vol.8,no.5,pp.515–525,2000. andE.W.Sayers,“GenBank,”NucleicAcidsResearch,vol.37,
[20] K.R.Rosendal,K.Wild,G.Montoya,andI.Sinning,“Crystal databaseissue,pp.D26–D31,2009.
structureofthecompletecoreofarchaealsignalrecognition [36] O.Weichenrieder,K.Wild,K.Strub,andS.Cusack,“Structure
particle and implications for interdomain communication,” and assembly of the Alu domain of the mammalian signal
ProceedingsoftheNationalAcademyofSciencesoftheUnited recognitionparticle,”Nature,vol.408,no.6809,pp.167–173,
StatesofAmerica,vol.100,no.25,pp.14701–14706,2003. 2000.
[21] C.Y.Janda,J.Li,C.Oubridge,H.Herna´ndez,C.V.Robinson, [37] E.S.Andersen,M.A.Rosenblad,N.Larsenetal.,“ThetmRDB
andK.Nagai,“Recognitionofasignalpeptidebythesignal and SRPDB resources,” Nucleic acids research., vol. 34, pp.
recognitionparticle,”Nature,vol.465,no.7297,pp.507–510, D163–168,2006.
2010. [38] M.Regalia,M.A.Rosenblad,andT.Samuelsson,“Prediction
[22] K. Wild, G. Bange, G. Bozkurt, B. Segnitz, A. Hendricks, of signal recognition particle RNA genes,” Nucleic Acids
and I. Sinning, “Structural insights into the assembly of Research,vol.30,no.15,pp.3368–3377,2002.
the human and archaeal signal recognition particles,” Acta [39] E. Iakhiaeva, J. Wower, I. K. Wower, and C. Zwieb, “The 5e
CrystallographicaSectionD,vol.66,no.3,pp.295–303,2010. motifofeukaryoticsignalrecognitionparticleRNAcontainsa
[23] O. N. Pakhomova, S. Deep, Q. Huang, C. Zwieb, and A. P. conservedadenosineforthebindingofSRP72,”RNA,vol.14,
Hinck,“SolutionstructureofproteinSRP19ofArchaeoglobus no.6,pp.1143–1153,2008.
fulgidus signal recognition particle,” Journal of Molecular [40] E. Iakhiaeva, J. Yin, and C. Zwieb, “Identification of an
Biology,vol.317,no.1,pp.145–158,2002. RNA-bindingdomaininhumanSRP72,”JournalofMolecular
[24] U. Ilangovan, S. H. Bhuiyan, C. S. Hinck et al., “A. fulgidus Biology,vol.345,no.4,pp.659–666,2005.
SRP54M-domain,”JournalofBiomolecularNMR,vol.41,no. [41] C. Darwin, “Modes of transition,” in The Origin of Species,
4,pp.241–248,2008. chapter6,JohnMurray,London,UK,1859.
[25] T. Hainz, S. Huang, and A. E. Sauer-Eriksson, “Interaction [42] S.J.GouldandE.S.Vrba,“Exaptation—amissingterminthe
ofsignal-recognitionparticle54GTPasedomainandsignal- scienceofform,”Paleobiology,vol.8,no.1,pp.4–15,1982.
recognition particle RNA in the free signal-recognition par- [43] S. Nolivos, A. J. Carpousis, and B. Clouet-d’Orval, “The K-
ticle,” Proceedings of the National Academy of Sciences of the loop,ageneralfeatureofthePyrococcusC/DguideRNAs,is
United States of America, vol. 104, no. 38, pp. 14911–14916, anRNAstructuralmotifrelatedtotheK-turn,”NucleicAcids
2007. Research,vol.33,no.20,pp.6507–6514,2005.
10 Archaea
[44] R. Stefl, L. Skrisovska, and F. H.-T. Allain, “RNA sequence- [60] J. D. Miller, H. D. Bernstein, and P. Walter, “Interaction
andshape-dependentrecognitionbyproteinsintheribonu- of E. coli Ffh/4.5S ribonucleoprotein and FtsY mimics that
cleoproteinparticle,”EMBOReports,vol.6,no.1,pp.33–38, of mammalian signal recognition particle and its receptor,”
2005. Nature,vol.367,no.6464,pp.657–659,1994.
[45] J.C.Politz,S.Yarovoi,S.M.Kilroy,K.Gowda,C.Zwieb,and [61] S.Althoff,D.Selinger,andJ.A.Wise,“Molecularevolutionof
T. Pederson, “Signal recognition particle components in the SRPcyclecomponents:functionalimplications,”NucleicAcids
nucleolus,”ProceedingsoftheNationalAcademyofSciencesof Research,vol.22,no.11,pp.1933–1947,1994.
theUnitedStatesofAmerica,vol.97,no.1,pp.55–60,2000. [62] S. Gribaldo and P. Cammarano, “The root of the universal
[46] T.S.MaityandK.M.Weeks,“AthreefoldRNA-proteininter- treeoflifeinferredfromancientlyduplicatedgenesencoding
face in the signal recognition particle gates native complex components of the protein-targeting machinery,” Journal of
assembly,” Journal of Molecular Biology, vol. 369, no. 2, pp. MolecularEvolution,vol.47,no.5,pp.508–516,1998.
512–524,2007. [63] P.F.Egea,S.-O.Shan,J.Napetschnig,D.F.Savage,P.Walter,
[47] H.Maeshima,E.Okuno,T.Aimi,T.Morinaga,andT.Itoh, and R. M. Stroud, “Substrate twinning activates the signal
“AnarchaealproteinhomologoustomammalianSRP54and recognition particle and its receptor,” Nature, vol. 427, no.
bacterial Ffh recognizes a highly conserved region of SRP 6971,pp.215–221,2004.
RNA,”FEBSLetters,vol.507,no.3,pp.336–340,2001. [64] A. Zelazny, A. Seluanov, A. Cooper, and E. Bibi, “The NG
[48] I.Tozik,Q.Huang,C.Zwieb,andJ.Eichler,“Reconstitution domainoftheprokaryoticsignalrecognitionparticlereceptor,
of the signal recognition particle of the halophilic archaeon FtsY, is fully functional when fused to an unrelated integral
Haloferaxvolcanii,”NucleicAcidsResearch,vol.30,no.19,pp. membranepolypeptide,”ProceedingsoftheNationalAcademy
4166–4175,2002. ofSciencesoftheUnitedStatesofAmerica,vol.94,no.12,pp.
[49] J. Yin, Q. Huang, O. N. Pakhomova, A. P. Hinck, and C. 6025–6029,1997.
Zwieb,“Theconservedadenosineinhelix6ofArchaeoglobus [65] E. Bibi, A. A. Herskovits, E. S. Bochkareva, and A. Zelazny,
fulgidussignalrecognitionparticleRNAinitiatesSRPassem- “Putative integral membrane SRP receptors,” Trends in Bio-
bly,”Archaea,vol.1,no.4,pp.269–275,2004. chemicalSciences,vol.26,no.1,pp.15–16,2001.
[50] A.Kuglstatter,C.Oubridge,andK.Nagai,“Inducedstructural [66] S.A.LadefogedandG.Christiansen,“AGTP-bindingprotein
changes of 7SL RNA during the assembly of human signal ofMycoplasmahominis:asmallsizedhomologtothesignal
recognitionparticle,”NatureStructuralBiology,vol.9,no.10, recognitionparticlereceptorFtsY,”Gene,vol.201,no.1-2,pp.
pp.740–744,2002. 37–44,1997.
[51] M. Sa´nchez, J.-M. Beckerich, C. Gaillardin, and A. [67] I.V.ShepotinovskayaandD.M.Freymann,“Conformational
Dom´ınguez,“IsolationandcloningoftheYarrowialipolytica changeoftheN-domainonformationofthecomplexbetween
SEC65 gene, a component of the yeast signal recognition the GTPase domains of Thermus aquaticus Ffh and FtsY,”
particle displaying homology with the human SRP19 gene,” Biochimica etBiophysica Acta, vol. 1597, no. 1, pp. 107–114,
Gene,vol.203,no.1,pp.75–84,1997. 2002.
[52] S. Yurist, I. Dahan, and J. Eichler, “SRP19 is a dispensable [68] T. Lichi, G. Ring, and J. Eichler, “Membrane binding of
component of the signal recognition particle in Archaea,” SRPpathwaycomponentsinthehalophilicarchaeaHaloferax
JournalofBacteriology,vol.189,no.1,pp.276–279,2007. volcanii,”EuropeanJournalofBiochemistry,vol.271,no.7,pp.
[53] R. W. Rose and M. Pohlschro¨der, “In vivo analysis of an 1382–1390,2004.
essentialarchaealsignalrecognitionparticleinitsnativehost,” [69] A.Haddad,R.W.Rose,andM.Pohlschro¨der,“TheHaloferax
JournalofBacteriology,vol.184,no.12,pp.3260–3267,2002. volcaniiFtsYhomologiscriticalforhaloarchaealgrowthbut
[54] C. Moser, O. Mol, R. S. Goody, and I. Sinning, “The signal doesnotrequiretheAdomain,”JournalofBacteriology,vol.
recognitionparticlereceptorofEscherichiacoli(FtsY)hasa 187,no.12,pp.4015–4022,2005.
nucleotide exchange factor built into the GTPase domain,” [70] J.Luirink,C.M.TenHagen-Jongman,C.C.vanderWeijden
ProceedingsoftheNationalAcademyofSciencesoftheUnited etal.,“AnalternativeproteintargetingpathwayinEscherichia
StatesofAmerica,vol.94,no.21,pp.11339–11344,1997. coli:StudiesontheroleofFtsY,”EMBOJournal,vol.13,no.
[55] P.J.RapiejkoandR.Gilmore,“EmptysiteformsoftheSRP54 10,pp.2289–2296,1994.
andSRαGTPasemediatetargetingofribosome-nascentchain [71] H.-J.Dong,J.-Y.Jiang,andY.-Q.Li,“Thedistinctanchoring
complexestotheendoplasmicreticulum,”Cell,vol.89,no.5, mechanismofFtsYfromdifferentmicrobes,”CurrentMicro-
pp.703–713,1997. biology,vol.59,no.3,pp.336–340,2009.
[56] R. J.Keenan, D. M. Freymann, P. Walter, and R.M. Stroud, [72] M. Mircheva, D. Boy, B. Weiche, F. Hucke, P. Graumann,
“Crystal structure of the signal sequence binding subunit of andH.-G.Koch,“Predominantmembranelocalizationisan
thesignalrecognitionparticle,”Cell,vol.94,no.2,pp.181– essential feature of the bacterial signal recognition particle
191,1998. receptor,”BMCBiology,vol.7,articleno.76,2009.
[57] R.T.Batey,R.P.Rambo,L.Lucast,B.Rha,andJ.A.Doudna, [73] E.deLeeuw,D.Poland,O.Moletal.,“Membraneassociation
“Crystalstructureoftheribonucleoproteincoreofthesignal ofFtsY,theE.coliSRPreceptor,”FEBSLetters,vol.416,no.3,
recognition particle,” Science, vol. 287, no. 5456, pp. 1232– pp.225–229,1997.
1239,2000. [74] E.deLeeuw,K.teKaat,C.Moseretal.,“Anionicphospholipids
[58] J.A.NewittandH.D.Bernstein,“TheN-domainofthesignal areinvolvedinmembraneassociationofFtsYandstimulateits
recognitionparticle54-kDasubunitpromotesefficientsignal GTPaseactivity,”EMBOJournal,vol.19,no.4,pp.531–541,
sequencebinding,”EuropeanJournalofBiochemistry,vol.245, 2000.
no.3,pp.720–729,1997. [75] R. Parlitz, A. Eitan, G. Stjepanovic et al., “Escherichia coli
[59] E.M.Cle´rico,A.Szymanska,andL.M.Gierasch,“Exploring signalrecognitionparticlereceptorFtsYcontainsanessential
the interactions between signal sequences and E. coli SRP and autonomous membrane-binding amphipathic helix,”
by two distinct and complementary crosslinking methods,” Journal of Biological Chemistry, vol. 282, no. 44, pp. 32176–
Biopolymers,vol.92,no.3,pp.201–211,2009. 32184,2007.