Shine–Dalgarno sequence - Wikipedia

The Shine–Dalgarno (SD) sequence is a ribosomal binding site in bacterial and archaeal messenger RNA, generally located around 8 bases upstream of the start ... Shine–Dalgarnosequence FromWikipedia,thefreeencyclopedia Jumptonavigation Jumptosearch RibosomalbindingsiteinprokaryoticmessengerRNA TheShine–Dalgarno(SD)sequenceisaribosomalbindingsiteinbacterialandarchaealmessengerRNA,generallylocatedaround8basesupstreamofthestartcodonAUG.[1]TheRNAsequencehelpsrecruittheribosometothemessengerRNA(mRNA)toinitiateproteinsynthesisbyaligningtheribosomewiththestartcodon.Oncerecruited,tRNAmayaddaminoacidsinsequenceasdictatedbythecodons,movingdownstreamfromthetranslationalstartsite. TheShine–Dalgarnosequenceiscommoninbacteria,butrarerinarchaea.[2]Itisalsopresentinsomechloroplastandmitochondrialtranscripts.Thesix-baseconsensussequenceisAGGAGG;inEscherichiacoli,forexample,thesequenceisAGGAGGU,whiletheshorterGAGGdominatesinE.colivirusT4earlygenes.[1] TheShine–DalgarnosequencewasproposedbyAustralianscientistsJohnShineandLynnDalgarno. Contents 1Recognition 1.1Translationstartsites 1.2Translationtermination 2Sequenceandproteinexpression 3Seealso 4References 4.1Furtherreading 5Externallinks Recognition[edit] Translationstartsites[edit] UsingamethoddevelopedbyHunt,[3][4]ShineandDalgarnoshowedthatthenucleotidetractatthe3'endofE.coli16SribosomalRNA(rRNA)(thatis,theendwheretranslationbegins)ispyrimidine-richandhasthespecificsequenceYACCUCCUUA.Theyproposedthattheseribosomalnucleotidesrecognizethecomplementarypurine-richsequenceAGGAGGU,whichisfoundupstreamofthestartcodonAUGinanumbermRNAsfoundinvirusesthataffectE.coli.[1]ManystudieshaveconfirmedthatbasepairingbetweentheShine–DalgarnosequenceinmRNAandthe3'endof16SrRNAisofprimeimportanceforinitiationoftranslationbybacterialribosomes.[5][6] GiventhecomplementaryrelationshipbetweenrRNAandtheShine–DalgarnosequenceinmRNA,itwasproposedthatthesequenceatthe3'-endoftherRNAdeterminesthecapacityoftheprokaryoticribosometotranslateaparticulargeneinanmRNA.[7]Basepairingbetweenthe3'-endoftherRNAandtheShine–DalgarnosequenceinmRNAisamechanismbywhichthecellcandistinguishbetweeninitiatorAUGsandinternaland/orout-of-frameAUGsequences.ThedegreeofbasepairingalsoplaysaroleindeterminingtherateofinitiationatdifferentAUGinitiatorcodons. Translationtermination[edit] In1973DalgarnoandShineproposedthatineukaryotes,the3'-endofthesmall18SrRNAmayplayaroleintheterminationofproteinsynthesisbycomplementarybasepairingwithterminationcodons.[8]Thiscamefromtheirobservationthatthe3'terminalsequencesof18SrRNAfromDrosophilamelanogaster,Saccharomycescerevisiae,andrabbitcellsareidentical:GAUCAUUA-3'OH.[9]Theconservationofthissequencebetweensuchdistantlyrelatedeukaryotesimpliedthatthisnucleotidetractplayedanimportantroleinthecell.Sincethisconservedsequencecontainedthecomplementofeachofthethreeeukaryoticterminationcodons(UAA,UAGandUGA)itwasproposedtohavearoleintheterminationofproteinsynthesisineukaryotes.Asimilarroleforthe3'endof16SrRNAinrecognisingterminationtripletsinE.coliwasproposedin1974byShineandDalgarnoonthebasisofcomplementarityrelationshipsbetweenthe3'-terminalUUA-OHin16SrRNAandE.coliterminationcodons.[citationneeded]InF1phage,aclassofvirusesthatinfectbacteria,thesequencecodingforthefirstfewaminoacidsoftencontainsterminationtripletsinthetwounusedreadingframes.[furtherexplanationneeded][10]Inacommentaryonthispaper,itwasnotedthatcomplementarybasepairingwiththe3'-terminusof16SrRNAmightservetoabortpeptidebondformationafterout-of-phaseinitiation.[11] Sequenceandproteinexpression[edit] MutationsintheShine–Dalgarnosequencecanreduceorincrease[12]translationinprokaryotes.ThischangeisduetoareducedorincreasedmRNA-ribosomepairingefficiency,asevidencedbythefactthatcompensatorymutationsinthe3'-terminal16SrRNAsequencecanrestoretranslation. Seealso[edit] Kozakconsensussequence,thesequencethattargetstheribosometotheinitiationcodoninEukaryotes. Bacterialtranslation Archaealtranslation References[edit] ^abcMalysN(2012)."Shine-DalgarnosequenceofbacteriophageT4:GAGGprevailsinearlygenes".MolecularBiologyReports.39(1):33–9.doi:10.1007/s11033-011-0707-4.PMID 21533668.S2CID 17854788. ^Benelli,D;Londei,P(January2011)."TranslationinitiationinArchaea:conservedanddomain-specificfeatures".BiochemicalSocietyTransactions.39(1):89–93.doi:10.1042/BST0390089.PMID 21265752. ^HuntJA(1970)."Terminal-sequencestudiesofhigh-molecular-weightribonucleicacid.The3'-terminiofrabbitreticulocyteribosomalRNA".BiochemicalJournal.120(2):353–363.doi:10.1042/bj1200353.PMC 1179605.PMID 4321896. ^ShineJ,DalgarnoL(1973)."Occurrenceofheat-dissociableribosomalRNAininsects:thepresenceofthreepolynucleotidechainsin26SRNAfromculturedAedesaegypticells".JournalofMolecularBiology.75(1):57–72.doi:10.1016/0022-2836(73)90528-7.PMID 4197338. ^DahlbergAE(1989)."ThefunctionalroleofribosomalRNAinproteinsynthesis".Cell.57(4):525–529.doi:10.1016/0092-8674(89)90122-0.PMID 2655923.S2CID 36679385. ^SteitzJA,JakesK(1975)."HowribosomesselectinitiatorregionsinmRNA:basepairformationbetweenthe3'-terminusof16SrRNAandthemRNAduringtheinitiationofproteinsynthesisinEscherichiacoli".ProcNatlAcadSciUSA.72(12):4734–4738.Bibcode:1975PNAS...72.4734S.doi:10.1073/pnas.72.12.4734.PMC 388805.PMID 1107998. ^ShineJ,DalgarnoL(1975)."Determinantofcistronspecificityinbacterialribosomes".Nature.254(5495):34–38.Bibcode:1975Natur.254...34S.doi:10.1038/254034a0.PMID 803646.S2CID 4162567. ^DalgarnoL,ShineJ(1973)."Conservedterminalsequencein18SrRNAmayrepresentterminatoranticodons".Nature.245(148):261–262.doi:10.1038/newbio245261a0.PMID 4202225. ^HuntJA(1965)."Terminal-sequencestudiesofhigh-molecular-weightribonucleicacid.Thereactionofperiodate-oxidizedribonucleosides,5'-ribonucleotidesandribonucleicacidwithisoniazid".BiochemicalJournal.95(2):541–51.doi:10.1042/bj0950541.PMC 1214355.PMID 14340106. ^PieczenikG,ModelP,RobertsonHD(1974)."Sequenceandsymmetryinribosomebindingsitesofbacteriophagef1RNA".JournalofMolecularBiology.90(2):191–214.doi:10.1016/0022-2836(74)90368-4.PMID 4375722. ^Anon(1976)."Signalsforproteinsynthesis".Nature.260(5546):12–13.Bibcode:1976Natur.260...12A.doi:10.1038/260012a0. ^JohnsonG(1991)."Interferencewithphagelambdadevelopmentbythesmallsubunitofthephage21terminase,gp1".JournalofBacteriology.173(9):2733–2738.doi:10.1128/jb.173.9.2733-2738.1991.PMC 207852.PMID 1826903. Furtherreading[edit] VoetDandVoetJ(2004).Biochemistry(3rd ed.).JohnWileyandSonsInc.pp. 1321–1322and1342–1343. HaleWG,MarghamJP,SaundersVAeds(1995)CollinsDictionaryofBiology,(2nded)Shine-Dalgarno(SD)sequence.p565. Lewin,B.(1994)GenesV.OxfordUniversityPress.pp179,269. AlbertsB,BrayD,LewisJ,RaffM,RobertsK,WatsonJD(1994)TheMolecularBiologyoftheCell(3rded.)pp237,461. MalysN,McCarthyJE(2011)."Translationinitiation:variationsinthemechanismcanbeanticipated".CellularandMolecularLifeSciences.68(6):991–1003.doi:10.1007/s00018-010-0588-z.PMID 21076851.S2CID 31720000. CicekMustafa,MutluOzal,ErdemirAysegul,OzkanEbru,SaricayYunus,Turgut-BalikDilek(2013)."SingleMutationinShine-Dalgarno-LikeSequencePresentintheAminoTerminalofLactateDehydrogenaseofPlasmodiumEffectstheProductionofanEukaryoticProteinExpressedinaProkaryoticSystem".MolecularBiotechnology.54(2):602–608.doi:10.1007/s12033-012-9602-z.PMID 23011788.S2CID 45230872.{{citejournal}}:CS1maint:multiplenames:authorslist(link) Externallinks[edit] https://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=eurekah.section.19320 vteProteinbiosynthesis:translation(bacterial,archaeal,eukaryotic)ProteinsInitiationfactorBacterial IF1 IF2 IF3 Archaeal aIF1 aIF2 aIF5 aIF6 EukaryoticeIF1 eIF1 B family eIF1A Y eIF2 α β γ eIF2B 1 2 3 4 5 kinase eIF2A eIF2D eIF3 A B C D E F G H I J K L M eIF4 A 1 2 3 E1 2 3 G 1 2 3 B H eIF5 EIF5 EIF5A 2 5B eIF6 EIF6 ElongationfactorBacterial/​Mitochondrial EF-Tu EF-Ts EF-G EF-4 EF-P TSFM GFM1 GFM2 Archaeal/​Eukaryotic a/eEF-1 A1 2 3 B P1 P2 P3 D E G a/eEF-2 Releasefactor Class1 eRF1 Class2/RF3 GSPT1 GSPT2 RibosomalProteinsCytoplasmic60Ssubunit RPL3 RPL4 RPL5 RPL6 RPL7 RPL7A RPL8 RPL9 RPL10 RPL10A RPL10-like RPL11 RPL12 RPL13 RPL13A RPL14 RPL15 RPL17 RPL18 RPL18A RPL19 RPL21 RPL22 RPL23 RPL23A RPL24 RPL26 RPL27 RPL27A RPL28 RPL29 RPL30 RPL31 RPL32 RPL34 RPL35 RPL35A RPL36 RPL36A RPL37 RPL37A RPL38 RPL39 RPL40 RPL41 RPLP0 RPLP1 RPLP2 RRP15-like RSL24D1 40Ssubunit RPSA RPS2 RPS3 RPS3A RPS4(RPS4X,RPS4Y1,RPS4Y2) RPS5 RPS6 RPS7 RPS8 RPS9 RPS10 RPS11 RPS12 RPS13 RPS14 RPS15 RPS15A RPS16 RPS17 RPS18 RPS19 RPS20 RPS21 RPS23 RPS24 RPS25 RPS26 RPS27 RPS27A RPS28 RPS29 RPS30 RACK1 Mitochondrial39Ssubunit MRPL1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 28Ssubunit MRPS1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 Otherconcepts AminoacyltRNAsynthetase Readingframe Startcodon Stopcodon Shine-Dalgarnosequence/Kozakconsensussequence Retrievedfrom"https://en.wikipedia.org/w/index.php?title=Shine–Dalgarno_sequence&oldid=1091885346" Categories:ProteinbiosynthesisHiddencategories:ArticleswithshortdescriptionShortdescriptionmatchesWikidataAllarticleswithunsourcedstatementsArticleswithunsourcedstatementsfromApril2016WikipediaarticlesneedingclarificationfromApril2016CS1maint:multiplenames:authorslist Navigationmenu Personaltools NotloggedinTalkContributionsCreateaccountLogin Namespaces ArticleTalk English Views ReadEditViewhistory More Search Navigation MainpageContentsCurrenteventsRandomarticleAboutWikipediaContactusDonate Contribute HelpLearntoeditCommunityportalRecentchangesUploadfile Tools WhatlinkshereRelatedchangesUploadfileSpecialpagesPermanentlinkPageinformationCitethispageWikidataitem Print/export DownloadasPDFPrintableversion Inotherprojects WikimediaCommons Languages العربيةDanskDeutschEspañolFrançaisGalego한국어ItalianoעבריתMagyarNederlands日本語PolskiPortuguêsРусскийไทยУкраїнськаTiếngViệt中文 Editlinks