TThhee RRNNAA WWoorrldld E. Westhof http://www-ibmc.u-strasbg.fr/upr9002/westhof/ Stabilization of Fossils of the hydrosphere stromatolites Decrease in the Organic matter Earth Number of From living organisms Formation Meteorite impacts 4.5 4.2 4.0 3.8 3.6 3.4 (x 109 ans) RNA WOLRD Global overview of all life RNA World The RNA World • Origin of life / central dogma paradox • DNA needs proteins to replicate • Proteins coded for by DNA • RNA can be code and machinery • Selex, aptamers • RNAs are remnants • Ancient and Essential RNA, Parts O O H H N N Bases O N O N Sugar (ribose) OH OH O O O O O Phosphate O P O O P O - O - 5’ 3’ DNA = modified RNA O O -O P O P O Base O Ribonucleoside O- O- H H H H triphosphates RNA OH OH NADP+ Thioredoxine (-SH)2 Ribonucleoside NADPH diphosphate + Thioredoxine + H -(S-S-) réductase O O -O P O P O Base O Deoxyribonucleoside O- O- H H H H triphosphates DNA OH H O O3' O O3' O O3' P P P O O5' O O5' O O5' Nucleic acids are negatively charged biopolymers ... 5!’ ADENINE (A) O O P O O O O THYMINE (T) (Uracil) OH O P O O O GUANINE (G) O O P O OH O O O OH CYTOSINE (C) O P O O O O OH O P O RNARNA O 3!’ Conformations of RNA •Primary structure of RNA similar to DNA •RNA, like DNA, can be single or double stranded, linear or circular. •Unlike DNA, RNA can exhibit different foldings •Different folds permit the RNAs to carry out specific functions in the cell H H H N N C H C N N Charge énamine imine H O O delocalization H C C N N H H lactame (forme céto) lactime (forme énol) H H + N N C C Tautomeric N N forms O O H C H C + N N Cytidine H H H H N N H H H N pKa = 4,2 N 3 + H+ H O H O N N S S O O Uridine H Protonation H H N pKa = 9,2 N 3 + H+ H O H O N N possibilities S S Adénosine H H H H N N N N H pKa = 3,5 N N 1 + H H + H H H N N N N S S Guanosine O O H O N N N H pKa = 2,1 H N 7 N 6 pKa = 9,2 N 1 H H H + H H+ H H H N N N N N N N N N H H H S S S H Guanine O O N N H N 6 N 1 H H H H N N N N N N Always H H Never S S Adénine H H H N N N N H seen N 6 N 1 H H N N seen N N S S Uracile H O O O H H H H N 4 N N 3 ou 2 O H O H O H N N N H S S S Cytosine H H H H N N N H H H H N 4 N N 3 ou 2 O H O H O H N N N H S S S H H N O CH3 N N H H3C Modified bases N N H H H N N N N N H have different S S 1-méthyladénine 7-méthylguanine O CH3 … N H N H H H N O H H H3C N N N N N H CH 3 N N O O S 2,2,7-triméthylguanine H H N N N N N H H H … 8-oxoadénine 8-oxoguanine H H N O H H N N electronic O H O N N H H H H H H N N N properties N N H H H Fapy-adénine Fapy-guanine H-bond characteristics N N 1,8 - 2 Å H H N H N d- d+ d- N H O N donneur accepteur O H N C 2,8 - 3 Å H N H 4 O 6 N C 3 N H N1 G Horizontal N N N O 2 H N 2 Interactions H H O 4 H N6 N Base pairing. U 3 N H N1 N A N N In helices O H H3C O H 4 N 6 Complementary N T 3 N H N Watson-Crick N 1 A N N O 55 ° 55 ° 10.5 Å Vertical interactions : stacking H O N H O N N N O N N H N N H N O N H H N N N N H H H H N O N H O N N O H N H O O H N N N N N O O N N H H Stacking forces • Driving Force : hydrophobic effect. • Not very specific •Partition in very polar regions (phosphates) & less polar ones (exocyclic groups of bases) History of the many roles of RNA Central dogma The flow of genetic information transcription translation DNA RNA Protein DNA notoriety Short history of RNA • Late 1800’s - 2nd kind of nucleic acid not in the nucleus (rRNA) • 1920’s - sugar for DNA vs RNA • 1958 - tRNA (Hoagland) • 1960’s - mRNA Relative Amount of RNA in E. coli rRNA 80% tRNA 15% mRNA 5% RNA •“Three” different types of RNA •mRNA - messenger RNA, specifies order of amino acids during protein synthesis •tRNA - transfer RNA, during translation mRNA information is interpreted by tRNA •rRNA – ribosomal RNA, combined with proteins aids tRNA in translation Ribosomal RNA (rRNA) Phylogeny of Life using SSU rRNA Discovery of catalytic RNA • Early 1980’s : • Tom Cech & Sidney Altman • Self-splicing group I introns and • Ribonuclease P P9.2 P9.1 360 P9.1a 380 370 A G G U G G A A A C GUAUG U U A A UC AAG G G U CGC C U CA C C 350 A • • • • • • • • • • • • • • • • • • • • • • • • • • G G UA UA U GA U U A GUUU C U A GCGG A GUG P13'' A U AU GA A U 390 400 340 P9b 330 P9a U A GGG AG U GG A G A A UC C UC UC C C U A G AC A 320 G C P5a G C 5´ U 3´ g C G U a U 130 U A A u A U 200 G C g 120 C G C G U P10 C g P13 190 P13 U A P5 U G C G C G U a U G C G 20 U a 410 A A U U G U u A C A A G u U A G c U A P9.0 A A G C G A P1 A u A C G G c U A C G G u 210 G C A 260 G c 180 G C P5c G C C G 110 A U P4 G C C A C G A A AGGGU A C G U 310 170 A U A C A U G C P7 G U C CG G A 140 U A U P14'' U G A U A A U G U U 160 P6 U A G C C G A A 270 A U C A A A U P5b G C A C A C G U A A G U 220 G U U G G U 100 G C U G U A A A C G P3 C G P6a C G C G A G 150 C G 250 A U A A U U G C A A A 300 U A G G U C G 280 U A U G C G C G P8 230 A U U A A U U A P14 P6b C G P8 C G P14 A U U A G C 240 U U A U 290 A UG U C U A A A P13' 40 P2 90 80 P230 A A A C A C C G U GG A C UA U UG A C G GA A A U U U GG UA U • • • • • • • • • • • • • • • • • • • • • U G C C U GGUA GC U A GU C UU U A A A C C AU P14' C A A A A 50 70 G P2 60 P2.1 Group I self-splicing introns Core structure 9 5 5' 3' P10 P5 G P9.0 P1 C G P4 5' P7 7 P6 P3 3 P8 2 6 8 CCaatatalylytictic CCoorree ooff GGrroouupp II intronsintrons Réaction de Transetransestérificationsterification !! Ribozyme H O O H P N O N OH O H N OH N O O G N O O O P O O O O P 5' O O OH OH 3' O U O O P OH O O O U O Exon 5' Second discovery of RNA • ncRNAs - functional RNA molecules rather than proteins; RNA other than mRNA (ex.XIST) • RNAi - RNA interference • siRNA- active molecules in RNA interference; degrades mRNA (act where they originate) • miRNAs - tiny 21–24-nucleotide RNAs; probably acting as translational regulators of protein-coding mRNAs (regulate elsewhere) Other Roles of RNA • stRNA - Small temporal RNA; (ex. lin-4 and let-7 in Caenorhabditis elegans : development • snRNA - Small nuclear RNA; includes spliceosomal RNAs • snoRNA - Small nucleolar RNA; most known snoRNAs are involved in rRNA modification • RNA world - RNA as catalyst Central dogma The flow of genetic information transcription translation DNA RNA X Protein ncRNA genes • Genomic dark matter • Ignored by gene prediction methods • Not in EnsEMBL • Computational complexity • ~10% of human gene count? RNA interference Intricate maturation pathways Implicated in chromatine remodelling Cleavage part of DICER Measuring device for 21 nt ONE Role of RNA in cells 1 Transcription tRNA DNA DNA mRNA Amino RNA acids polymerase RNAr 1 anticodon protein RNA Polypeptide nucleotides chain 2 2 Translation codon ribosome Proteins mRNA Versatility of RNA functions • Not only messenger RNAs (alternative splicing) • Number & variety of non-coding RNAs : ribosomal RNAs, snRNAs, snoRNAs,and numerous regulator RNAs.