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Canada I Bibliotheque Nationale Du Canaaod a Collections Development Branch F Direction Du Developpement Des Collections \'S t . .CANADIAN tHESES ON MICROFICHE ISBN THESES CANADIENltES SUR MICROFICHE 1 + National Library of Canada i Bibliotheque nationale du Canaaod a Collections Development Branch f Direction du developpement des collections Canadian Theses on Service des theses canadiennes ' Microfiche Service sur microfiche v t Ottawa, Canada K1A-0N4 ^ '1 NOTICE ' • AVIS . The quality of this microfiche .is heavily dependent La qualite de cette microfiche depend grandement de upon the quality of tine original thesis submitted for la qualite de la these soumise au microfilmage Nous microfilming Every effort has been made to ensure avonstout fait pour assurer une qualite supeneure the highest quality of reproduction possible de reproduction * If pages are missing, contact the university which S'll mancfue des pages, veuillez commumquer granted the degree, J i avec I'universite qui a confere le grade * Some pages may have indistinct print especially La qualite depression de certaines pages peut if the original pages were typed with a poor typewriter laisser a desirer, surtout'si les page(s onginales ont ete ribbon or if the university sent us a-poor photocopy* dactylographies a I'aide d'un ruban use ou si I'univer­ site nous a fait parvemr une photocopie de mauvaise qualite Previously copyrighted materials (journal" articles, Les documents qui font deja I'objet d'un droit published tests, etc.) are not filmed. d'auteur (articles de revue, examens publies, etc ) nep sont pas microfilmes •Reproduction in full or in part of this film is gov­ La reproduction, meme pajrtielle, de ce microfilm erned by the Canadian Copyright Act, RSC 1970, est soumise a la Loi cafiadienne sur le droit d'auteur, c C-30, Please read the .authorization forms which • SRC 19/0, c C-30 Veuillez prendre connaissance des accompany this thesis formules d'autonsation qui acc^rmpagnent cette these THIS "DISSERTATION LA THESE A ETE HAS BEEN MICROFILMED MICROFILMEE TELLE QUE EXACTLY AS RECEIVED NOUS L'AVONS RECUE 'NL-339 (r. 8?/08~) " Canada It -> / » RIBOSOMAL- RNA STRUCTURE AND EVOLUTION REVEALED BY NUCLEOTIDE,SEQUENCE, ANALYSIS y by ^ /fjp* Murray N. Schnare Submitted in partial fulfillment of the-^requirementsfor the degree of Doctor of Philosophy at DalHousie University Department of Biochemistry r * Dalhousie.llniversity s Halifax,'Nova Scotia . June,' 1984 \ * •/" •» • 1 • J .- c n»(*y) • - r . ' '. TABLE OF CJTTENTSW '* ' * • . Page LIST OF FIGURES X • • • "- • • • ' x I trST.OF TABLES ...". , •.....» *n > c ABSTRACT f,. ; , : "xi~i 1 v LIST OF ABBREVIATIONS .'. ; '. xiv ACKiftwLEDGEMENT S • .'.*.,. .' ^ xvi INTRODUCTION . ' v . v ^* J ' -- 1. The Ribosome: A Macromolecular Complex of Central ' „ * ' " .Biological Importance".., ' >..;'. 1 , 2. • Structure'of Ribos„omes and their RNa Components * 2 2.1. Diversity.in Ribosome and Ribosomal RNA t * m * Structure : : , 2 " 2.2'. SecondaryStructure of LSU and SSU"RNAs v..*4 • " „ ,2.3. * Modified Nucleoside Components of Ribosomal v * - ' ' RNA , ' 5 - ' x > "5. *" Evolutionary Origin of Cow Molecular Weight •Ribosomal RNAs * -...."? 7 .3.1'. Ribosomal RNA Gene Organization .^..'..y^, , 7 • (b(a)) j' ArchaebacteriaEubacterial rRNl ArRN GeneA Genes s <.* ,87 (c) Chlo/oplast rRNA Genes ....4 ' 9 (d) Eukarfyotic Nuclear rRNA Genes .., *... 10 (e) Mitochondrial rRNA Genes ...* <. 13 3.2. "Structural Homology between Low Molecular Weight rRNAs and the Ends'of E.' coli '23S rRNA 16 i (*• 1 -(v)^~ i > ' •: • F 3.3. " Transcribed Spacers and Variable Regions in " rRNA Genes *. ." 18 •v. « 3.4. The Ribosomal RNAs of Crithidia fasciculata 19* 4. * Phyl ogenetic, Relationships'and Small Subunit ^ , - - v • ^ • - Ribosomal RNAs rT 20 4.1. Phyl ogenetic CIassifications 20 4.-2. 'Evolutipnary^flrigin of Mitochondria 21 ' 4.3. Structure, Evplutio'n and Function of the'3'-Terminal Sequence of SSU RNA .y .-..V... 25 METHODS , . ' * 1, Preparation of Viable Wheat Embryos 28 2* Germination of Wheat Embryos" V '. 29 3. Isolation of Wheat "Mitochondrial and ^ ' Wheat Cytosol Total RNA '.,.... 29' 4. Isolation of Total RNA from Crithidia fasciculata 32 . ., . • - b, 5.' Salt Fractionation of Total RNA. 33 6. Isolation of Wheat Cytosol Ribosomal Sufcumts 34 7. Isolation of Wheat Mitochondrial Rlbpsomal Subumts ,t ..' .« 35 8.* Isolation of Crittfidia fasciculata Ribosomal v Subunits ••., 1 35 fcr, '' .- / } 9. Analytical Polyacrylamide Gel Electrophoresis .J 36 , ,,\^ • 10." Purification-of Individual Ribosomal RNAs ..* 38 v~ * * < / * *•."',.., ., Pa9e •10.1. Pol yacryl amide Gel Electrophoresis v ........... 38 (a) Electroptioretic Separation of Low '• Molecular Weight Ribosblnal RNAs t 39 . ' • - , » (b) Electrophoretic Separation of High . Molecular Weight Ribosomal RNAs 40 sc .10.2. El ectropho.retic-Elation .' ' 40 > 10.3." Homogemzation ©f Gel Slices ....- 42 11. Preparation of Purified End-Labelled , 'Ribosomal RNAr *. 43 11.1 5-'-End Labelling .. .yff. ;••••• 43 11.2. 3'-End Labelling^. , 43 r - 1L3. Purification^ End-Labelled RtfA ,..' 44 11.4. .Elution ofrRNA from Sequencing Gels , 45- 12. Analysis of Terminal Nucleoside Residues \ 46 ) ... ^ . {3. Rapid Sequencing of End-Labelled Ribosomal RNA 47 13.1. Chemical'Sequencing Reactions „••••. jfl7 (a) G "Reaction > ^ 47 •(b) A>£ Reaction ..' .*!... .\.*. w49 (c) U. Reaction ,»' ..; 49-' (d) C Reaction- .- ....' ' 4? (e) Alternate C Reaction 5& -" - (f) Strand Scission Reaction 51 - (g) Partial Alkali'Digestion < * 51 ' lis.2\ Partial Enzymatic Digestions '. 52 'i i ( - ;•' .'••••>,' V* - .• ' ' . , . ' -(vn)- , • - « ' v •• .„ Page - • * , 13\3. .Sequencing" Gels 53 (a) Electrophoresis-' '...:.„.. *. .53 ^* (b) Autoradiograph'y f ". 54 , -. |(c) Interpretation of Gels '....: *:.." 55 • 14. v Mdj^Lified Nucleoside' Analysis * „...".....-. 57 14. fc' Unlabel led Marker Nucleotide* : '. 57 • 14.2. Analysis of Urn form! y-3?P-Labelled- Small rRNAs :.., .'...." * '58 . "14.3. Modified Nucleosides Near the ^--Terminus of SSU RNA .' :S .' .59 15. Preparation and Detection of Intermojecular^ " * - '« . ' * ' * " RNA:RNA Compl exes V,.' ., ,.... „. ty) c 16. 'Preparation of-Nitrocellulose Filters Containing' Restriction Fragntents of Wheat Mitochondrial DNA...... 61 - . 17. , RNA: DNA Southern Hybridization .' , -..' '...62 ** • -' " ' -^ » RESULTS . ' * • . "^ 1 1. Wheat Mitochondrial and Cytosol RNAk '. ..* * 63 • 2- Crithidia fasc/icfulata Ribos^mal RNA - ,.'.. 63 3- Intermolecul ar RN^RJIA Complexes^ •. ! .. 65 4. 3'-Terminal Sequence of Crithidia fascicu.lata • 18S rRNA , 67 *. • 5^ 3'-Terminal Sequences of Wheat Mitochondrial and •Wheat Cytosol 18S rRNAs 72 ul » -*. r t - * • * •^ -(vii/i)- * * t ; 4. V . • < Page . « 5.1. Primary Sequences,.- f ; 72 5.2.\ Patterns of Post-Tr%anscriptional Modification 77 * 6. Heterologous rRNA-mtDNA Hybridization ...*...* 84 7. ' Numbered Orientation of Wheat Mitochondrial 18S and 5S Ribosomal RNA Genes '. : 86 8. 3'-Terminal Sequences of Wheat Mitochondrial „ • and Cytosol 20S rRNA? »., 87 9.. Complete Nucleotide Sequence of Crithidia fasciculata 5.8S rRNA .-, 90 "9.1., End Groups .... \ 90 9.2. Modified Nucleoside Constituents ; 91 A 9.3. / Primary Sequence I , 91 10. Primary'-Structure of Four Novel Small rRNAs from Crithidia fasciculata k...., 97 10.1. Primary Sequence ' : 97 ':* 11^2. End Groups 104 t\ 10.3: Modified Nucleosides , 106 f> * '.* < * » DISCUSSION 1. Evolutionary Relationships Based on Ribosomal RNA Sequence Comparisons ., 108 2. Structure and Evolution of the 3'-Terminus of n * " Eukaryotic SSU RNA- , 114 3. Functions of the 3'-Terminus of Eukaryotic SSU , RNA 119 / -(ix). Page, 4. The Evolutionary Origin of Wheat Mitochondria 1.2ft 4.1. Evidence Supporting a Abacterial Origin .*.-. 124 (a) Evidence Prior to this Work ?..... 124 4 '(b) Evidence Presented in this Thesis 125 ": (c)- Recent'Evidence .*...'....... *$£ 130 4.2. Non-Eubacterial Characteristics of Wheat Mitochondrial rRNA Genes .* 130 (a) Ribosomal RNA Gene Organization 130 (bj Wheat Mitochondrial 5S rRNA * '., 131 (c) Initiation of Translation 131 (d) Ribosomal RNA Processing • ,.. 132 4.3 Conclusions About Mitochondrial Evolution 133 5. Low Molecular Weight rRNAs and Their Analogues 136 5\1 , The'3VTerminus of LSU RNA *.. 136 5.2 Crithidia fasciculata 5.8S rRNA '. 139 5.3 Novel Small'rRNAs from Crithidia fasciculata1 143 6. Concluding Remarks and Future Prospeqts ." 144 BIBLIOGRAPHY -.. 148 Jf Htx). LIST OF FIGURES ,. ' "Page Ribosomal RNA g'ene organization ...,.- 6 Arrangement of the rRNA genes in diverse- mitochondrial genomes ..' 14 ' '* ' Polyacryl amide gel electrophoretic profiles of total * > RNA from wheat cytosol and wh'eat mitochondria *.. 64 Polyacrylamide gel electrophoretic profiles of 9 • Crithidia fasciculata rRNA 66 Detection of intermolecul ar RNA:RNA complexes 68 Autoradiogram of chemical sequencing gel (20%) of 3'-end-labelled Crithidia 18S rRNA ..' '. 70 Autoradiograms of chemical sequencing gels (10%)' of 3'-end-labelled Crithidia 18S 'rRNA' t *J1 —;—r~ Sequance of the first 91 nucleotide rjaidues at'the 3'-end of Crithidia 18S-rRNA f 73 Autoradiograms of sequencing gels (20%.) of 3'-e,nd- labelled wheat mitochondrial and E.. coli SS.U RNAs 75 Autoradiograms of sequencing gels (10%)*of 3'- end-labelled wheat mitochondrial, wheat cytosol and E. coli SSU'RNAs ' 76 Potential secondary structure near the 3'-terminus of SSU RNA '. .* 78 *i Autoradiograms of tic plates which establish the presence of pm3U at analogous positions in -^- E. coli 16S and "wheat mitochondrial 18S rRNAs •*. 83 « - « f • * » -(xi)- . ***'.'# Page * t> i Autoradiograms showing the'results
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