RNA Catalysis, Structure and Folding Chair: E. Westhof RNA Meeting 2008 Berlin. Density courtesy David Shechner

Transcription

1 RNA Catalysis, Structure and Folding Chair: E. Westhof RNA Meeting 2008 Berlin Density courtesy David Shechner

2 Catalysis implies very precise chemistry: Bringing several atoms at the correct distances and with the proper orientations in the right environment >> Folding and architecture come into play >> Related difficulties in sorting out chemistry & folding for evaluating mutation effects (identifying the correct rate-limiting step)

3 Three families of catalytic RNAs 5 -phosphate + 3 OH A PETITS RIBOZYMES RNase P O - OH - OH Mg 2+ O S O H 2 C P O O R O OH Mg 2+ C 2,3 -cyclic/ 3 -phosphate + 5 OH 3,5 ou 2,5 - O3' / - O2' OH INTRONS O

4 Magnesium ions: where and how many, if any? RNase P O - OH - OH A OH PETITS RIBOZYMES Mg 2+ O S O P O R Mg 2+ C O H 2 C O - O3' / - O2' OH INTRONS O

5 General acid-base catalysis: Roles of nucleic acid bases A, C, G

6 Thematic Workshop (Anna Marie Pyle) on RNA catalytic strategies This morning session more focused on folding and architecture

7 More and more structures available (never enough ) Natural ribozymes - several group I introns (+ chaperone CYT18) - several hammerhead structures - hairpin ribozyme - HDV ribozyme - Artificial ribozymes - Diels-Adler - Ligase - Flexizyme

8 Each structure can be parsed in modules RNA architecture (3D) = non- Watson-Crick base pairs

9 Use of recurrent modules or motifs K-turn T-loop A-minor Family C 3-w jct Nucleic Acids Res 34, 6587 (2006)

10 The most frequent RNA-RNA recognition motif: the A-minor motif Type I Sugar-Sugar Trans Type II Sugar-Sugar Cis Nissen et al. P.N.A.S. 98, 4899 (2001)

11 Always the same contacts involving two adenines but presented by various modules 3

12 Junctions between helices are key for RNA ARCHITECTURE & CATALYSIS

13 Importance of long- range contacts: Control at a distance David Lilley, Martha Fedor, Anastasia Khvorova

14 Nomura map Brodersen et al. J. mol. Biol. 316, 725 (2002) Primary r-proteins bind at RNA junctions

15 Natural ribozymes - group II (#114 Kevin Keating, Pyle s lab) - the VS ribozyme (#109 Jonathan Ouellet, Lilley s lab) Artificial ribozymes - a class I ligase (#110 David Schechner, Bartel s lab)

16 #114 First structure of a group II intron Published by AAAS N. Toor, Keating, Taylor & Pyle, Science 320, (2008)

17 Ligation reaction M. P. Robertson & W.G. Scott, Science 315, (2007)

18 RNA sensors and riboswitches - TPP, purine, SAM riboswitches - glms riboswitch (catalytic) - Mg(II) sensor - SAMII riboswitch -

19 RNA sensors and riboswitches - Lysine riboswitch (#119 Sacha Serganov, Patel s lab) - FMN riboswitch (see poster #593)

20 Structure of the SAM-II riboswitch bound to S-adenosylmethionine Gilbert, Rambo, Van Tyne, & Batey, Nature Struct & Mol Biol 15, 177 (2008)

21 Recognition of thiamine via H-bonding and stacking Serganov et al. 441, 1167 (2006) Recognition of NEGATIVE charges via Magnesium ions

22 Techniques for studying BINDING & FOLDING #116 Kathrin Lang (Micura s lab)

23 Workshop on Structural Biology Xray, NMR, EM, SAXS, modeling: -What type of questions can/cannot be addressed with each technique and how to integrate them? -What are the future challenges? Jamie Cate, Friedrich Foerster, Anna Pyle, Holger Stark, Jamie Williamson Open round table discussion Workshop on High-Throughput Sequencing SOLEXA, 454, SOLiD: introducing the technologies -Comparing technologies -Rate-limiting steps -The future:technologies and accessibility Open round table discussion

24 The proportion of noncoding DNA broadly increases with developmental complexity Vertebrates Ciona (urochordate) Invertebrates Plants Complex fungi (Neurospora) Simple eukaryotes (yeasts, plasmodium, Dictyostelium) Prokaryotes Vertebrates Urochordate Invertebrates Plants Complex fungi Simple eukaryotes Prokaryotes J.S. Mattick Nature Reviews Genetics 5, (2004). R.J. Taft, M. Pheasant and J.S. Mattick, Bioessays 29, (2007)

25 New bioinformatic tools: towards automatic modelling of 3D structure #118 Marc Parisien (Major s lab) Structures in non-catalytic non-coding RNAs : Xist RNA #113 Malgorzata Duszczyk (Sattler s lab)

26 nothera new frontier: telomerase RNA #115 Nak-Kyoon Kim (Feigon s lab) From Theimer et al. Mol Cell 27, 869 (2007)

27 How do catalytic RNA molecules emerge & evolve?

28 How a protein replaces a RNA Module Structure of a tyrosyl-trna synthetase splicing factor bound to a group I intron RNA Paukstelis, Chen, Chase, Lambowitz & Golden, Nature 451, 94 (2008)

29 RNaseP : two folds, one reaction P12 P13 L11/12 E. coli Type A 3' P10.1 L11/12 P12 B. subtilis Type B 3' 5' 5' P14 P10/ P11 P9 P1 R19 P10/ P11 P9 P1 P19 P7 P8 P4 P2 P18 P7 P8 P4 P2 P5 P3 P5 P3 P15.2 P6 P5.1 P15.1 P17 P16 P15 P15 L15 L15

30 Catalytic mechanism(s) and its regulation Unexpected and unrelated catalytic reactions - 2,5 versus 3,5 (#117 B.Masquida (lab)) - GTP versus G as cofactor (#112 Quentin Vicens (Cech s lab)) - 2,3 linkage instead of 2,5 (#111 Duncan Smith (Konarska s lab))

31 Recent awareness: Minor changes in local folds and environments can lead to changes in types of reaction

32 3D Modules are recurrent And can exchange (swap) Different modules interact through identical interaction protocols This molecular neutrality together with the RNA chemical lability must have contributed to the success of the RNA World