16S ribosomal RNA - Wikipedia

Universal primers 16SribosomalRNA FromWikipedia,thefreeencyclopedia Jumptonavigation Jumptosearch RNAcomponent ThisarticleismissinginformationaboutRfamSSU_rRNA_bacteria,SSU_rRNA_archaea.Pleaseexpandthearticletoincludethisinformation.Furtherdetailsmayexistonthetalkpage.(December2020) Molecularstructureofthe30SSubunitfromThermusthermophilus.ProteinsareshowninblueandthesingleRNAstrandinorange.[1] 16SribosomalRNA(or16SrRNA)istheRNAcomponentofthe30Ssubunitofaprokaryoticribosome(SSUrRNA).ItbindstotheShine-DalgarnosequenceandprovidesmostoftheSSUstructure. Thegenescodingforitarereferredtoas16SrRNAgeneandareusedinreconstructingphylogenies,duetotheslowratesofevolutionofthisregionofthegene.[2]CarlWoeseandGeorgeE.Foxweretwoofthepeoplewhopioneeredtheuseof16SrRNAinphylogeneticsin1977.[3]Multiplesequencesofthe16SrRNAgenecanexistwithinasinglebacterium.[4] Contents 1Functions 2Structure 3Universalprimers 3.1PCRandNGSapplications 3.2Hypervariableregions 4Promiscuityof16SrRNAgenes 516Sribosomaldatabases 5.1EzBioCloud 5.2RibosomalDatabaseProject 5.3SILVA 5.4GreenGenes 6References 7Externallinks Functions[edit] Likethelarge(23S)ribosomalRNA,ithasastructuralrole,actingasascaffolddefiningthepositionsoftheribosomalproteins. The3′-endcontainstheanti-Shine-Dalgarnosequence,whichbindsupstreamtotheAUGstartcodononthemRNA.The3′-endof16SRNAbindstotheproteinsS1andS21whichareknowntobeinvolvedininitiationofproteinsynthesis[5] Interactswith23S,aidinginthebindingofthetworibosomalsubunits(50Sand30S) Stabilizescorrectcodon-anticodonpairingintheA-sitebyformingahydrogenbondbetweentheN1atomofadenineresidues1492and1493andthe2′OHgroupofthemRNAbackbone. Structure[edit] SSURibosomalRNA,bacteriaandarchaea.FromWoese1987.[6] Universalprimers[edit] The16SrRNAgeneisusedforphylogeneticstudies[7]asitishighlyconservedbetweendifferentspeciesofbacteriaandarchaea.[8]CarlWoese(1977)pioneeredthisuseof16SrRNA.[2]Itissuggestedthat16SrRNAgenecanbeusedasareliablemolecularclockbecause16SrRNAsequencesfromdistantlyrelatedbacteriallineagesareshowntohavesimilarfunctionalities.[9]Somethermophilicarchaea(e.g.orderThermoproteales)contain16SrRNAgeneintronsthatarelocatedinhighlyconservedregionsandcanimpacttheannealingof"universal"primers.[10]MitochondrialandchloroplasticrRNAarealsoamplified. ThemostcommonprimerpairwasdevisedbyWeisburgetal.(1991)[7]andiscurrentlyreferredtoas27Fand1492R;however,forsomeapplicationsshorterampliconsmaybenecessary,forexamplefor454sequencingwithtitaniumchemistrytheprimerpair27F-534RcoveringV1toV3.[11] Often8Fisusedratherthan27F.Thetwoprimersarealmostidentical,but27FhasanMinsteadofaC.AGAGTTTGATCMTGGCTCAGcomparedwith8F.[12] Primername Sequence(5′–3′) Ref. 8F AGAGTTTGATCCTGGCTCAG [13][14] 27F AGAGTTTGATCMTGGCTCAG [12] U1492R GGTTACCTTGTTACGACTT [13][14] 928F TAAAACTYAAAKGAATTGACGGG [15] 336R ACTGCTGCSYCCCGTAGGAGTCT [15] 1100F YAACGAGCGCAACCC 1100R GGGTTGCGCTCGTTG 337F GACTCCTACGGGAGGCWGCAG 907R CCGTCAATTCCTTTRAGTTT 785F GGATTAGATACCCTGGTA 806R GGACTACVSGGGTATCTAAT [16][17] 533F GTGCCAGCMGCCGCGGTAA 518R GTATTACCGCGGCTGCTGG 1492R CGGTTACCTTGTTACGACTT [18] PCRandNGSapplications[edit] Inadditiontohighlyconservedprimerbindingsites,16SrRNAgenesequencescontainhypervariableregionsthatcanprovidespecies-specificsignaturesequencesusefulforidentificationofbacteria.[19][20] Asaresult,16SrRNAgenesequencinghasbecomeprevalentinmedicalmicrobiologyasarapidandcheapalternativetophenotypicmethodsofbacterialidentification.[21]Althoughitwasoriginallyusedtoidentifybacteria,16Ssequencingwassubsequentlyfoundtobecapableofreclassifyingbacteriaintocompletelynewspecies,[22]orevengenera.[7][23] Ithasalsobeenusedtodescribenewspeciesthathaveneverbeensuccessfullycultured.[24][25] Withthird-generationsequencingcomingtomanylabs,simultaneousidentificationofthousandsof16SrRNAsequencesispossiblewithinhours,allowingmetagenomicstudies,forexampleofgutflora.[26] Hypervariableregions[edit] Thebacterial16Sgenecontainsninehypervariableregions(V1–V9),rangingfromabout30to100basepairslong,thatareinvolvedinthesecondarystructureofthesmallribosomalsubunit.[27]Thedegreeofconservationvarieswidelybetweenhypervariableregions,withmoreconservedregionscorrelatingtohigher-leveltaxonomyandlessconservedregionstolowerlevels,suchasgenusandspecies.[28]Whiletheentire16Ssequenceallowsforcomparisonofallhypervariableregions,atapproximately1,500basepairslongitcanbeprohibitivelyexpensiveforstudiesseekingtoidentifyorcharacterizediversebacterialcommunities.[28]ThesestudiescommonlyutilizetheIlluminaplatform,whichproducesreadsatrates50-foldand12,000-foldlessexpensivethan454pyrosequencingandSangersequencing,respectively.[29]Whilecheaperandallowingfordeepercommunitycoverage,Illuminasequencingonlyproducesreads75–250basepairslong(upto300basepairswithIlluminaMiSeq),andhasnoestablishedprotocolforreliablyassemblingthefullgeneincommunitysamples.[30]FullhypervariableregionscanbeassembledfromasingleIlluminarun,however,makingthemidealtargetsfortheplatform.[30] While16Shypervariableregionscanvarydramaticallybetweenbacteria,the16Sgeneasawholemaintainsgreaterlengthhomogeneitythanitseukaryoticcounterpart(18SribosomalRNA),whichcanmakealignmentseasier.[31]Additionally,the16Sgenecontainshighlyconservedsequencesbetweenhypervariableregions,enablingthedesignofuniversalprimersthatcanreliablyproducethesamesectionsofthe16Ssequenceacrossdifferenttaxa.[32]Althoughnohypervariableregioncanaccuratelyclassifyallbacteriafromdomaintospecies,somecanreliablypredictspecifictaxonomiclevels.[28]Manycommunitystudiesselectsemi-conservedhypervariableregionsliketheV4forthisreason,asitcanprovideresolutionatthephylumlevelasaccuratelyasthefull16Sgene.[28]Whilelesser-conservedregionsstruggletoclassifynewspecieswhenhigherordertaxonomyisunknown,theyareoftenusedtodetectthepresenceofspecificpathogens.InonestudybyChakravortyetal.in2007,theauthorscharacterizedtheV1–V8regionsofavarietyofpathogensinordertodeterminewhichhypervariableregionswouldbemostusefultoincludefordisease-specificandbroadassays.[33]Amongstotherfindings,theynotedthattheV3regionwasbestatidentifyingthegenusforallpathogenstested,andthatV6wasthemostaccurateatdifferentiatingspeciesbetweenallCDC-watchedpathogenstested,includinganthrax.[33] While16Shypervariableregionanalysisisapowerfultoolforbacterialtaxonomicstudies,itstrugglestodifferentiatebetweencloselyrelatedspecies.[32]InthefamiliesEnterobacteriaceae,Clostridiaceae,andPeptostreptococcaceae,speciescanshareupto99%sequencesimilarityacrossthefull16Sgene.[34]Asaresult,theV4sequencescandifferbyonlyafewnucleotides,leavingreferencedatabasesunabletoreliablyclassifythesebacteriaatlowertaxonomiclevels.[34]Bylimiting16Sanalysistoselecthypervariableregions,thesestudiescanfailtoobservedifferencesincloselyrelatedtaxaandgroupthemintosingletaxonomicunits,thereforeunderestimatingthetotaldiversityofthesample.[32]Furthermore,bacterialgenomescanhousemultiple16Sgenes,withtheV1,V2,andV6regionscontainingthegreatestintraspeciesdiversity.[8]Whilenotthemostprecisemethodofclassifyingbacterialspecies,analysisofthehypervariableregionsremainsoneofthemostusefultoolsavailabletobacterialcommunitystudies.[34] Promiscuityof16SrRNAgenes[edit] Undertheassumptionthatevolutionisdrivenbyverticaltransmission,16SrRNAgeneshavelongbeenbelievedtobespecies-specific,andinfallibleasgeneticmarkersinferringphylogeneticrelationshipsamongprokaryotes.However,agrowingnumberofobservationssuggesttheoccurrenceofhorizontaltransferofthesegenes.Inadditiontoobservationsofnaturaloccurrence,transferabilityofthesegenesissupportedexperimentallyusingaspecializedEscherichiacoligeneticsystem.UsinganullmutantofE.coliashost,growthofthemutantstrainwasshowntobecomplementedbyforeign16SrRNAgenesthatwerephylogeneticallydistinctfromE.coliatthephylumlevel.[35][36]SuchfunctionalcompatibilitywasalsoseeninThermusthermophilus.[37]Furthermore,inT.thermophilus,bothcompleteandpartialgenetransferwasobserved.Partialtransferresultedinspontaneousgenerationofapparentlyrandomchimerabetweenhostandforeignbacterialgenes.Thus,16SrRNAgenesmayhaveevolvedthroughmultiplemechanisms,includingverticalinheritanceandhorizontalgenetransfer;thefrequencyofthelattermaybemuchhigherthanpreviouslythought. 16Sribosomaldatabases[edit] The16SrRNAgeneisusedasthestandardforclassificationandidentificationofmicrobes,becauseitispresentinmostmicrobesandshowsproperchanges.[38]Typestrainsof16SrRNAgenesequencesformostbacteriaandarchaeaareavailableonpublicdatabases,suchasNCBI.However,thequalityofthesequencesfoundonthesedatabasesisoftennotvalidated.Therefore,secondarydatabasesthatcollectonly16SrRNAsequencesarewidelyused.Themostfrequentlyuseddatabasesarelistedbelow: EzBioCloud[edit] EzBioClouddatabase,formerlyknownasEzTaxon,consistsofacompletehierarchicaltaxonomicsystemcontaining62,988bacteriaandarchaeaspecies/phylotypeswhichincludes15,290validpublishednamesasofSeptember2018.Basedonthephylogeneticrelationshipsuchasmaximum-likelihoodandOrthoANI,allspecies/subspeciesarerepresentedbyatleastone16SrRNAgenesequence.TheEzBioClouddatabaseissystematicallycuratedandupdatedregularlywhichalsoincludesnovelcandidatespecies.Moreover,thewebsiteprovidesbioinformaticstoolssuchasANIcalculator,ContEst16Sand16SrRNADBforQIIMEandMothurpipeline.[39] RibosomalDatabaseProject[edit] TheRibosomalDatabaseProject(RDP)isacurateddatabasethatoffersribosomedataalongwithrelatedprogramsandservices.TheofferingsincludephylogeneticallyorderedalignmentsofribosomalRNA(rRNA)sequences,derivedphylogenetictrees,rRNAsecondarystructurediagramsandvarioussoftwarepackagesforhandling,analyzinganddisplayingalignmentsandtrees.Thedataareavailableviaftpandelectronicmail.Certainanalyticservicesarealsoprovidedbytheelectronicmailserver.[40]DuetoitslargesizetheRDPdatabaseisoftenusedasthebasisforbioinformatictooldevelopmentandcreatingmanuallycurateddatabases.[41] SILVA[edit] SILVAprovidescomprehensive,qualitycheckedandregularlyupdateddatasetsofalignedsmall(16S/18S,SSU)andlargesubunit(23S/28S,LSU)ribosomalRNA(rRNA)sequencesforallthreedomainsoflifeaswellasasuiteofsearch,primer-designandalignmenttools(Bacteria,ArchaeaandEukarya).[42] GreenGenes[edit] 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Externallinks[edit] UniversityofWashingtonLaboratoryMedicine:MolecularDiagnosis|BacterialSequencing TheRibosomalDatabaseProject RibosomesandRibosomalRNA:(rRNA) SILVArRNAdatabase Greengenes:16SrDNAdataandtools EzBioCloud vteRibosomalRNA/ribosomesubunitsArchaea(70S)Large(50S): 5S23SSmall(30S): 16SBacteria(70S)Large(50S): 5S23SSmall(30S): 16SEukaryotesCytoplasmic(80S)Large(60S): 5S5.8S28SSmall(40S): 18SMitochondrial(55S)Large(28S): MT-RNR2,16SMT-tRNAValSmall(39S): MT-RNR1,12SChloroplast(70S)Large(50S): 5S4.5S23SSmall(30S): 16SRibosomalproteins(Seearticletable) Retrievedfrom"https://en.wikipedia.org/w/index.php?title=16S_ribosomal_RNA&oldid=1092023433" Categories:RibosomalRNAMetagenomicsHiddencategories:WebarchivetemplatewaybacklinksCS1:longvolumevalueArticleswithshortdescriptionShortdescriptionmatchesWikidataArticlestobeexpandedfromDecember2020 Navigationmenu Personaltools NotloggedinTalkContributionsCreateaccountLogin Namespaces ArticleTalk English Views ReadEditViewhistory More Search Navigation MainpageContentsCurrenteventsRandomarticleAboutWikipediaContactusDonate Contribute HelpLearntoeditCommunityportalRecentchangesUploadfile Tools WhatlinkshereRelatedchangesUploadfileSpecialpagesPermanentlinkPageinformationCitethispageWikidataitem Print/export DownloadasPDFPrintableversion Languages CatalàČeštinaEspañolFrançaisGalego한국어BahasaIndonesiaItalianoქართულიMagyarМакедонски日本語PortuguêsRomânăРусскийУкраїнська中文 Editlinks