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Bioinformatic

By Allen Baker,2014-07-18 02:16
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Bioinformatic

    Bioinformatic

;zebrafish

    ;JieMeia,bJianfangGui,b,

    ;StateKeyLaboratoryofFreshwaterEcologyandBiotechnology,InstituteofHydrobiology,

    ;ChineseAcademyofSciences,Wuhan430072,China

    ;GraduateSchooloftheChineseAcademyofSciences,Beijing100049,China ;Receivedforpublication8June2007;revised25September2007;accepted17October2007

    ;Abstraet

    ;Claisthefirstsubcomponentofclassicalpathwayinthecomplementsystemandamajorlinkbetweeninnateandacquiredimmuni

    ;ties,Theglobular(gClq)domainsimilarwithClqwasalsofoundinmanynoncomplementClqdomaincontaining(ClqDC)proteins

    ;whichhavesimilarcrystalstructuretothatofthemultifunctionaltumornecrosisfactor(TNF)ligandfamily,andalsohavediversefunc

    ;tions,Inthisstudy,weidentifiedatotalof52independentgenesequencesencodingClqdomaincontainingproteinsthroughcompre

    ;hensivesearchesofzebrafishgenome.cDNAandESTdatabases,Incomparis

onto31orthologousgenesinhumananddifierentnumbers

    ;inotherspecies.asignificantselectivepressurewassuggestedduringvertebra

    domaincon teevolution.DomainorganizationofClq

    ;taining(ClqDC)proteinsmainlyincludesaleadingsignalpeptide,acollagenlikeregionofvariablelength,andaCterminalClqdo

    ;main,Therearel1highlyconservedresidueswithintheClqdomain,amongwhich2areinvariantwithinthezebrafishgeneset.Amore

    ;extensivedatabasesearchesalsorevealedhomologousClqDCproteinsinothervertebrates.invertebratesandevenbacterium.butno

    ;homologoussequencesforencodingClqDCproteinswerefoundinmanyspeciesthathaveamorerecentevolutionaryhistorywith

    ;zebrafish.Therefore.furtherstudiesonClqdomaincontaininggenesam

    ongdifferentspecieswillhelpusunderstandevolutionary ;mechanismofinnateandacquiredimmunities,

    ;Keywords:ClqDCproteins;globular(gClq)domain;collagenstalk;TNF/C1qfamily;phylogeneticanalysis

    ;Introduction

    ;Clq,assubcomponentofthecomplementC1complex,

    ;hasbeenrevealedtoinvolveinseveralotherimmunologi.

    ;calprocessesfKishoreandReid,2000;Kishoreeta1.,

    ;2004b).andmanyadditionalClqdomaincontaining

    ;fClqDCproteinshavebeenidentifiedinrecentyears

;fAlbe~ineta1..2000).TheseClqDCproteinshaveex

    ;tremelydiversefunctions,suchasactinglikehormones ;fTakamatsueta1.,1993;Maedaeta1.,2002),contributing ;totheinteractionofthecellwithextracellularmatrices ;(TomTangeta1.,2005),recognizingtargetsforseveral ;immunologicalprocesses(Navratileta1.,2001),orcon

    ;nectingasinglecalcifiedotolithtothesensoryepithelium ;Correspondingauthor.Fax:+862768780123

    ;E-mailaddress:jfgui@inb.ac,cn

    ;fMurayamaeta1..2002).Inhuman.atotalof31inde

    ;pendentClqDCgenesequenceshavebeenscreenedfrom ;thehumangenome.Basedonsequencehomology,func

    ;tionalrelatedness,andsimilaritiesindomainstructureand ;intron.exonPattern,theClqDCproteinshavebeenfurther ;classifiedintothreemajorsubfamiliesA,BandC(Tom ;Tangeta1..2005).

    ;Recently,weidentifiedanovelmemberofClqDCpro

    ;teinsfromcmciancarl3(Carassiusauratus),andfoundthat ;theCarassiusauratusovary..specificClq..1ikefactor, ;Ca0Clq.1ikefactor,wasspecificallyexpressedinthe ;ovaryfChenandGui,2004).Zebrafish(Daniorerio),asa ;smallfish,hasbeenthoughttobeanidealmodelforfunc

    ;tionalgenomics(Alestrometa1.,2006).Tofurtheridentify ;theClqDCproteingenesandrevealtheirbiologicalfunc

    ;tions,weperformedrecursivesearchesinthezebrafish ;genomeandproteindatabasesbytheknownC1qDCpro

    ;

    ;

    ;18JieMeieta1./JournalofGeneticsandGenomics3520081l724

    ;teinsastheinitialqueries.Astheresult.atotalof52inde

    ;pendentC1qDCgenesequenceswerescreenedintheze

    ;brafishgenome.Subsequently,theirstructuralcharacteri

    ;zation.functionaldiversificationandevolutionarysignifi

    ;cancewereanalyzedanddiscussed.Becausezebrafish ;genomehasbeenrevealedtoencode1argenumbersof ;componentsthatmediateapoptosisandinflammationin ;vertebratesincludinghumans(InoharaandNunez,2000; ;Aravindeta1..2001),itisveryimportantforustoidentify ;theClqdomaincontainingproteingenesinzebrafishand ;tounderstandtheirfunctionsandevolutionaryrelationship ;betweenzebrafishandhuman.Here.wereportedthebio

    ;informaticidentificationdatainzebrafish. ;Materialsandmethods

    ;Phylogeneticstudies

    ;ToobtainthecompletesetofzebrafishC1qDCproteins. ;weperformedrecursivesearchesusingknownClqDC ;proteinsastheinitialqueries.Wefirstidentifiedhomolo

    ;gousproteinsfromNCBIbvsearching”Clq.Danio”in

    ;proteinandnucleotidedatabases.Novelgeneswerealso ;searchedfromthesesameandzebrafishgenomedatabases ;bvtBLASTn.ClustalWwasusedtogeneratemultiplese

    ;quencealignmentfMSA1foragivensetofhomologous ;sequencesfThompsoneta1..1994).ThisMSAfilewas ;usedastheinputtoTreeTop,aprogramthatgeneratesph

    ;ylogenetictrees(phylip,phylograms)(http://www.gene

    ;bee.msu.su/genebee.htm1)basedontheoutputfromaClu

    ;stalWalignmentfBrodskiieta1..1995)andBoxSha

    ;deServerrhttp://www.ch.embnet.ore_Jsoflware/B0Xform. ;htm1).

    ;DiscoveringClqDCsinotherspecies

    ;C1qDCproteinsinotherspecieswerealsosearched ;fromtheGenBankdatabasefhttp://www.ncbi.nlm.nih.gov) ;Theiraccessionnumberslistasfollows:Strongylocentro. ;tuspurpuratus(purpleseaurchin):AAKll302(gi: ;12964750,Sp,ClqDC1),AAK11303(gi:12964752,Sp, ;C1qDC2),AAG16425(gi:10280597,Sp,C1qDC3),AAK

    ;11309(gi:12964764,Sp,ClqDC4),AAK11305(gi: ;12964756.Sp.ClqDC5);Bacilluscereus:AAP09230fgi: ;29895949,Bc,ClqDC1),AAP09231(gi:29895950,Bc. ;ClqDC2),AAP09378(gi:29896097,Bc,ClqDC3);Ory. ;ziaslatipes(medaka):AU179091(gi:13427928,OL.Clq

    ;DC1),AU178957(gi:13427793,OL,ClqDC2),AU

    ;176806(gi:13425642,OL,ClqDC3);7fl”rubripes

    ;(Fugu):CA588785(gi:25133363,TR,ClqDC1),CA

    ;330768(gi:24548866,TR,ClqDC2);Carassiusauratus: ;AY662672(gi:50379965CA,ClqDC1),AY583317(gi: ;46406029,CA,ClqDC2);Cyprinuscarpio(commoncarp): ;AB127584(gi:47971185,CC.ClqDC1).

    ;GenerationofcompletesetofzebrafishClqDCproteins ;andtheircommonstructuralfeatures

    ;ThroughcomprehensivesearchesinzebrafishEST. ;cDNA.andgenomedatabases.atotalof52independent ;ClqDCgenesequenceswerescreened.AsshowninTable ;1.thesizesofzebrafishClqdomaincontainingproteins

    ;varyfroml57aa(Cbln1)tol,730aafCblnl-2),and50of ;themcontainasingleCterminalClqdomainbesides

    ;ClqTNF4andZgc112213includetwotandemClqdo

    ;mainsfFig.1).ExceptinPde43andRiken.thegClqdo

    ;maininotherClqDCproteinslocatesattheendof ;Cterminus.DomainorganizationofClqDCproteins ;mainlyincludesaleadingsignalpeptide,acollagenlike

    ;regionofvariablelength.andaCterminalClqdomain.

    ;AmongthezebrafishClqDCproteins,8simultaneously ;containsignalpeptide,collagenandC1Q,17containsig

    ;nalpeptideandC1Q,and7containcollagenandC1Q, ;whereas20onlycontainC1O.InEmilin1.1,1-2,2.1,2.2 ;and3.1aswellasMultimerin2.1and2.2.thereisanEMI ;domain.anovelcysteinerichdomainofEmilinsandother

    ;extracellularproteins.Inaddition,someproteinsinclude ;coiledcoilandtransmembranedomain,Incontrasttoonly ;onememberwithoutsignalpeptideinhuman.thereare27 ;proteinsthatdon’thavesignalpepfideinzebrafish.Several

    ;genesinhuman,suchasClqTNF3,ClqTNF5,ClqTNF8 ;andCbln3.didnotfindinzebrafish.butmorenovel ;C1qDCproteingenesequenceswererevealedinzebrafish ;fTable1).Interestingly,thenumberofGXYrepeatsin ;zebrafishClqDCproteinsis20.40.60and100respec

    ;tively.whereasitvariesfrom14to153inhuman. ;SequencecomparisonofClqdomainsamongzebrafish ;C1qDCproteins

    ;Analignmentof54Clqdomainsfromzebrafish52 ;ClqDCproteinsf2ClqdomainsfromC1qTNF4and ;Zgc112213revealedtheobviousconservationanddiver

    ;genceamongthem.AsshowninFig.2.considerablevari

    con ;abilityoccursatsomepositions.butseveralwell

    ;servedregionscanbedistinguishedintheconserved ;3-strandsandconnectingloops(Kishoreeta1.,2004a).A ;totalof11highlyconservedresiduesareobserved.and2 ;ofthem(positionsG63,Y65)areinvariantinallzebrafish ;Clqdomains.

    ;PhylogeneticandevolutionaryanalysisofClqDCfamily ;proteins

    ;Basedonphylogenetictreeanalysis,zebrafishC1qDC ;proteinswerefurtherclassifiedintothreesubfamilies,such ;asClqDCAsubfamily,C1qDCBsubfamilyand

    ;ClqDCCsubfamily(Fig-3).Incomparisonwithhuman ;

    ;rIIable1

    ;ZebrafishClq?-domain?-containingproteins ;JieMeieta1./JournalofGeneticsandGenomics35(2008)l724

    ;NameProteinsize(aa)AnnotationChrom.1ocationGenBankaccession ;(becontinuedonnextpage)

;

    ;20JieMeietal~Joinnalf}fGeneticsandGenomics35(2008)l724

    ;(Continued) ;0200400600800 ;C1qdomain

    ;NH2——??

    ;NH2——————???

    ;NH2

    ;NH2

    ;120014001600180 ;Cbln21

    ;C1qTNF1,6

    ;NH2.-—?—?

    ;NH2_.—————??

    ;NH2

    ;NH2

    ;NH2

    ;NH2——?—?—_.?

    ;SignalpeptideandClqdomain

    ;NH2-—_.?

    ;NH2?—————_.-

    ;NH2

;NH2

    ;NH2

    ;NfI2

    ;NH2

    ;NH2

    ;Collagen-likeregionandC1qdomain

    ;NH2_|—?——_.?

    ;NH2

    ;NH2

    ;NH2

    ;NH2

    ;Pde43

    ;Cbln12

    ;Adiclql;Clq12.1;Clql4 ;Bzlg18.11

    ;ClclDC1

    ;Crf1.2:Gliacolin1.2.3 ;Emilin3.1

    ;Multimerin2.2:Emilin2.1 ;C1qTNF4;Zgcl12213 ;Cbin1.1.11.34

    ;Acrpl;C1q13;Zgcgl810,113062,109903

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