Consensus structure and evolution of 5S rRNA*

volume 11 Number 3 1983 Nucleic Acids Research Consensus structure and evolution of SS rRNA* Hans KOntzd, Birgjt Piechulla and Ulrica Hahn + Max-Planck-Institut for experimentcDe Median, Abteilung Oieinie, Hennann-Rein-Str. 3, D-3400 Gflttingen, FRG Received 23 November 1982; Revised and Accepted 5 January 1983 INTRODUCTION The 5S rRNA component of the large ribosomal subunit (1) is a suitable marker molecule to study pre-cambrian phylogeny: a comparison of 5S rRNA sequences from eukaryotes, eubacteria, archaebacteria and organelles (2-14) has revealed a considerable conservation of primary (15,16) and secondary (17-20) structure. Here we present a general consensus structure for all types of 5S rRNAs. Our model is in agreement with previously published secondary structure models for eubacterial (19,20), eukaryotic cytosolic (18,19) and archaebacterial (7) molecules, and in addition presents all conserved nucleotides in fixed positions. The observed group-specific deletions and base pair interactions support the phylogenetic grouping of 5S rRNA molecules based on nucleotide substitution data. MUTUODS 5S rRNA was extracted from the snail Arlon rufus, purified by preparative gel electrophoresis and sequenced by chemical cleavage methods as described (21). Methods used for computer-aided construction of dendrograms have been reported in detail (16,25). C I R L P r w i Limited, Oxford, England. 893 ABSTRACT A consensus structure model of 5S rRNA presenting all conserved nucleotides In fixed positions has been deduced from the primary and secondary structure of 71 eubacterial, archaebacterial, eukaryotic cytosolic and organellar molecules. Phylogenetically related groups of molecules are characterized by nucleotide deletions in helices III, IV and V, and by potential base pair interactions in helix IV. The group-specific deletions are correlated with the early branching pattern of a dendrogram calculated from nucleotide substitution data: the first major division separates the group of eubacterial and organellar molecules from a second group containing the common ancestors of archaebacterial and eukaryotic/cytosolic molecules. The earliest diverging branch of the eubacterial/organellar group includes molecules from Thermus thermophllus, T. aquaticus, Rhodospirilium rubrum, Paracoccus denitrifioans and wheat mitochondria. Nucleic Acids Research RESULTS AMD DISCUSSION Fig. 1 shows an alignment of selected 5S rRNA sequences representative for the groups of metazoa [sequence 1 ] , protozoa [19,20], plants [32], archaebacteria [41-46], eubacteria [47,50,56,60,61,67-69], chloroplasts [63] and mitochondria [71] . The alignment is similar, but not Identical, to previously published schemes (16,19) due to the inclusion of more sequence data. The consensus structure of Fig. 2A is based on the alignment of 71 5S rRNA sequences (2-14) and contains 70 positions where either A,U,G,C or a i 2 3 ft 5 6 - 123ll56789O12-3l| 5678-901234 J678901-23ll56789O123l! 5678-9012 1 2 3 * 5 1 7 8 9 0 12-\b 567890121*1 567—890-1 2tl< ^67890123l| ^678901 211* ^6-789 3I1 567890 6 1 1 1 2 01211! ^678901 2"jll ^6 1 CAGGGUCGGGCCUGGUU AGU-ACUUGGAUGGGAGACCGCCUGGOAAU-ACC QOOU-GCUGUAGGCUUU 1 19 CGCCUUAAGGCUGGGUU—AGU-ACUAAGCUGCGGGACCGCUUOGOAAG-UCC CAGU-GUCGACAGCCU- 19 20 CGGGACAGGGCCCGOAU AGU-ACUGGGCUGGGGGACCGCCCGGOAAG-UCCUUA00OU-0CUGUCAGCU— 2 0 2 7 CUCCUAAGAGCCUGACC-OAGU-AGUOUAGUGCGUGACCAUACGCOAAA-CUC AOGU-GCUGCAAUCU— 2 7 3 2 CGUGCUUGGGCOAGAGU AOU-ACUAGGAUGCGUGACCUCCUGGGAAG-UUC CCOU-OUUOCAUUCCC- 3 2 111 CCCGCCUGCGUUCCGOU-CAGU-ACUGCAGUGCGCGAGCCUCUGGGAAA-DCC OQUUCGCCGCCUACU— l> 1 l>3 ACACCUCACOUGGAUCA-CGCU-ACUOACCUACGCOAGUCCUCGGOAAA-UCA UCCUCOCUOCUAUUGUU ^ 3 llll CCUCCU-GCGUAUUGCG-irUGU-ACUOUAUGCCGCGAGOGUACGGOAAG-CGC AAUAUGCUCUUACOACU lift ftj CC-GCUCACGUUAGUOO OGC-CGUG0AUACCGU0AG0AU-CCGCAOC-CCC---ACUAAGCU0COAUGGQU b} k6 UCUUUUCGCGUUUUGUUUGUGU-ACUAUGGGtrUCCO-OUCUAUQOGAAU-UUC AUUUAOCUGCOAGCUUU ft6 <tj CGCCGUAGCGC-COA-U GGU-AGUGUGC-GQUCU-CCCCAUGCGA-G-AGU ACGGAACUGCCAGGCAU ft7 5O CGAUGCAUCGC-CGA-U GGU-AGUGUGG-OGUUU-CCCCAUGUCA-A-OAU CUCG-ACCAUAOAGCAU 5 0 5 6 CUCUAUUACGO-UGA-A—OAU-AUU ACUGAOGU OAGA-A-AAU AGCAAGCUGCCAOUU— 5 6 5 8 CUCUAAUGUGC-UGA-U—GOU-ACUGCAG-GGGAAGCC-CUGUGGA-GAAOU AOOUCOACGCUGGCU— 5 8 60 CCCCAUAOCGC-COA-U—GGUUACUGUAA-CCGGGAGGUUGUGGOA-G-AOU ACGUCGCCGCCGUOA— 6 0 6 1 CAUACCUGCGG-CAA-C—GAU-AGCUCCC-GGGUAGCCGGUCGCUA-A-AAU AGCUCGACGCCAGOUC- 6 1 6 3 CACUACUGCGO-UGA-G GAU-ACOGUAO-GGGAGCUCCUGCGGAA-A-AAU AGCUCCGCGCCAGAAU. 6 3 6 7 UCCCGUAGCGC-CAA-U—GGU-ACUGCG—UCAAAAGA-CGUCOOA-O-AGU AOCUCACCGCCAGACC- 6 7 68 GAGCCCUGCGC-CAA-U—GGU-ACOGCC—UCUUAAGG-CGUGGGA-G-AOU AGCUCGCCGCCAGGCCU 6 8 6 9 CGCGCCAGCGC-CGA-U—GGU-ACUGGC—GCACOACC-GCUCGGA-O-AOU ACOUCGGUGCGOGGGA- 6 9 7 1 UCGUCyUGCGC-CAU-A—UGU-ACUG- —-AAAUUOUU---CGGGA-Q-ACA UCQUCAAAGCCCGGAAA 7 1 1231156789012311567—890-123"! 567890123115678901231156-789 7 8 9 0 1 OI23I1567890123ft 56 1 2 1 1 Figure 1. Alignment of 21 selected 5S rRNA sequences. The nucleotlde numbers refer to the consensus structure of Fig. 2, the sequence numbers refer to the l i s t of organisms shown in Fig. 4. 894 - 123ft 56789012-~)ft 5 6 7 8 - 9 0 1 21ft 567890 l - 2 T l 567890123ft 5 6 7 8 - 9 0 ' 2 Vt 567890 1 GUCUACGGO-CAUACC-ACCCUGAACGCGC-CCGAUCUCCU-CUGAUC-UCGG AAGCUAAG 1 19 GCUGUCGGC-CAUACU-AAGGUGAAAACAC-CGGAUCCCAU-UCGAAC-'JCCO AAGUUAAG 19 2O GCUCACGGC-CAUACC-GDGUCOAAUGCAC-CGGAUCUCUU-CUGACC-UCCG AAGUUAAG 2 0 27 GGUIKHJGGC-CAUAUC-UACCAGAAAGCAC-CGUUUCCCGU-CCGAUCAACIJG UAGUUAAG 2 7 32 GOAUGCGAU-CAUACC-AGCACUAAAGCIC-CGGAUCCCAU-CAGAAC-BCCG AAGUUAAO 3 2 111 UUAAGGCGCC-CAUAGC-GGUGGGGUUACUC-CCGUACCCAUCCCGAAC-ACGG AAGAUAAG ft 1 ft 3 —UCAAUACCGGC-CACAGC-AGGUGUGUCACAC-CCGUUCCCAUUCCGAAC-ACGG AAGUUAAG ft 3 lift GGCAACGGU-CAUAGC-AGCAGGGAAACAC-CAGAUCCCAUUCCGAAC-UCGA CGGUUAAG ftft l»5 —GCCCACCCGGU-CAUAGU-GAGCGOGCAACAC-CCGGACUCAUUUCGAAC-CCGG AAGUUAAO It} k6 UAOGUUUGGCGGU-CAUAGC-OAUGG0GUAUCAC-CUGGUCUCGUUUCGAUC-CCA0 AAGUUAAG ft6 <(7 —UGCCUCGCGGC-CGUAGC-GCGCUGGUCCCAC-CUGACCCCAUGCCGAAC-UCAG AAGUGAAA IfJ 5 0 —UGUUCUGUGACGAGUAGUGGCAUUGGAA-CAC-CUGAUCCCAUCCCOAAC-UCAG AGGUGAAA 5 0 56 UUGGUGGU—AUAGC-AUAGAGGUCACAC-CUGUUCCCAUGCCGAAC-ACAG AAGUUAAG 5 6 58 UCCAGUGUC-UAUGAC-UUAOAGGUAACAC-UCCUUCCCAUUCCGAAC-AGGC AGGUUAAG 5 8 6 0 --GUUACGGCGGC-UAUAGC-GUGGGGGAAACGC-CCGGCCGUAUAUCGAAC-CC0O AAGCUAAG 6 0 61 UCCUGGUGUC-UAUGGC-GGUAUGCAACCACUCUGACCCCAUCCCGAAC-UCAG UUGUGAAA 6 1 6 3 -UAUUCUGGUGCUCCUAGGC-GUA0AGGAACCAAACCAAUC-CAUCCCOAAC-U0GG UGOUUAAA 6 3 67 GUCUGGUOQC-CAAAGC-ACGAGCAAAACAC-CCOAUCCCAUCCCOAAC-UCGO CCOUUAAG 6 7 6 8 -UGGCCUCQUOGU-CAUUGC-GCGCUCGAAACAC-CCOAUCCCAUCCCGAAC-UCGG CCGUGAAA 6 8 69 AAUCCCCCOUGCC-CAUAGC-GCCGUOOAACCAC-CCGUUCCCAUUCCGAAC-ACGG AAGUGAAA 6 9 71 -AAACCGQGCACUACCGUGA-GACGUGAAAACAC-CCGAUCCCAUUCCGACC-UCGAUAUAUAUGUGGAA 7 1 Nucleic Acids Research purine or pyrimidine nucleotide is conserved in more than 80 % of all sequences. The consensus sequence is folded according to the five helix model (18,19), and potential base pairs shown in straight lines are conserved in all molecules, with few exce (...truncated)