A hierarchical model for evolution of ribosomal RNA

1. A hierarchical model for evolution of ribosomal RNA Konstantin Bokov and Sergey Steinberg Université de Montréal 1

2. The ribosome is a universal machine producing proteins LARGE SUBUNIT GROWING PROTEIN - addition of new peptides to the growing protein chain (in PTC); - correct decoding of the messenger RNA (in DR); - precise movement along the messenger RNA; - coordination of the work of all co-factors and ligands; PTC P A TRANSPORT RNA SMALL SUBUNIT DR 5’ MESSENGER RNA 2

3. The evolution of Life on Earth directly depends on the emergence of the ribosome ! Protein World 3

4. The ribosome and LUCA Bacteria Archaea Eukarya Last Universal Common Ancestor 4

5. Small subunit Large subunit + + proteins RNA proteins RNA RNA+proteins Protein-WORLD RNA-WORLD RNA-body Functionality of the ribosome depends primarily on its RNA 5

6. F F MODERN RIBOSOME Major periods in the evolution of the ribosomal RNA Unlimited reshuffling of RNA chains F PROTO RIBOSOME Restricted step-wise increase of the ribosome size 6

7. Preserve functional structure ! gene sequence insertion 3’ 3’ 5’ 5’ 7

8. Accommodation of an insertion gene sequence gene sequence insertion Broken Unstable Stable 8

9. General principle of insertion: Structural integrity of more ancient elements cannot be dependent on the presence of more recently acquired elements. 9

10. 5’ 3’ 3’ 5’ Integrity of each strand of a double helix depends on the presence of the other strand 10

11. The A-minor motif as an evolutionary determinant A-minor motif 23S rRNA Nissen, P., Ippolito, J.A., Ban. N., Moore, P.B., Steitz, T.A. (2001) RNA tertiary interactions in the large ribosomal subunit: the A-minor motif. Proc Natl Acad Sci U S A.No 98(9), pp. 4899-4903. 11

12. In a newly emerged element: 1. The 3’- and 5’-termini must be close to each other2. For each double helix, both strands must be present3. When such element forms an A-minor interaction with the other elements of the ribosome, it must provide the adenosine stack and not the double helix 12

13. PROTO- RIBOSOME core 2-nd last acquisitions Last acquisitions Dismantling the ribosomal RNA: removal of those elements that are qualified as the most recent acquisitions of the ribosomal structure MODERN RIBOSOME 13

14. Dismantling the structure of the 23S rRNA 14

15. Inter-domainA-minorinteractions double helix A-min stack of adenosines 15

16. Dismantling the structure of the 23S rRNA 16

17. The symmetrical structure in Domain V is the proto-ribosome P-site A-site t-RNA 17

18. The network of dependencies does not contain cycles 54 59 18

19. If the orientations of all A-minor interactions in the 23S rRNA were chosenrandomly, the probability of a cycle-free arrangement would be P< 10-9.The absence of cycles of dependency is a fundamental characteristic of the 23S rRNA, which is directly related to the particular trajectory of its emergence. 19

20. Growing support for PTC 20

21. Appearance of the protuberances and of the small subunit 22

22. What about 16S rRNA? SSU LSU 21

23. The hypothetical structure of the primordial ribosome and two tRNAs 25

24. Small world... 26

25. Acknowledgment We appreciate the help of NSERC and CIHR for financing this project.

26. presentation

27. Chain of A-minor interactions Non-covalent dependency Double helix is older than stack of A-s packing in its minor groove E-coli, 23S E-coli, 23S E-coli, 23S A-stack (in red) A-stack (in red) A-stack (in red) H69 H92 H71 H71 H68 H69 H95 H92 H93 H95 H74 H93 H74 H68 A

28. C Pseudoknot B A The loop of a stem-loop structure (A) forms a double-helix (B) with a region outside this stem-loop for example with another stem-loop (C) B

29. Pseudoknots in the 23S rRNA - local - non-local C

30. Long-distance pseudoknots in the 23S rRNA 33 40 40 D

31. The approach is applicable

32. Along-groove packing” motif as a mean of structural fitting E-coli, 23S H25 minor groove G17-C523 H2 (G-C) G539-U554 H25 (G-U) H2 minor groove Along-groove packing motif F

33. Along-groove packing motif G

34. AGPM-s in 23S rRNA H

35. What about evolutionary deletions ? X B evolution A C =A-D L

36. Accommodation must not provoke structure weakening ? M

37. Additional Non-covalent dependency (A-min) E-coli, 23S E B yellow A-stacks A In PCK WC helices D E C D B C A The element containing stack of adenosines is non- covalently dependent on its complimentary WC helix A A Notion of dependency Covalent dependency E-coli, 23S A Core C B B A C Core The new RNA insertion covalently dependson the structure where it emerged N

38. Domain-V is the most ancient part of the ribosome P

39. 16S mitochondrial versus prokaryotes Only prokaryotes Mito and prokaryotes R

40. 23S mitochondrial versus prokaryotes Only prokaryotes S Mito and prokaryotes

41. Dismantling versus evolution MODERN RIBOSOME PROTO- RIBOSOME MODERN RIBOSOME PROTO- RIBOSOME T

42. AGPMs in the ribosome of E.coli 47 25 19 11 54 26 26 11 45 36 27 57 40 51 20 40

43. The evolution of Life on Earth directly depends on the emergence of the ribosome ! Protein World 2