17 . 1 Roles of RNA Molecules

1. 17.1Roles of RNA Molecules Ref: Ch. 5 Mount: Bioinformatics • Protein synthesis: ribosomal RNA transfer RNA messenger RNA • Catalysis e.g. ribozymes iii. Regulatory molecules

2. 17.2Interactions of RNA Molecules Nucleic acid interactions • complementary base pairing Protein interactions • Shape • Charge • Hydrophobicity iii. Regulatory molecules

3. 5’ 3’ 17.3Shape of RNA Molecules Self-complementary regions undergo complementary base pairing - depends on the formation of loops - 5’ end of one part of the molecule aligned with 3’ end of other part • Hydrophobicity

4. 17.4Types of Structures

5. 17.4Types of Structures

6. 17.4Types of Structures

7. 17.4Types of Structures

8. 17.4Types of Structures

9. 17.4Types of Structures

10. 17.5Complex Interactions Pseudoknot

11. 17.5Complex Interactions Kissing hairpins

12. 17.5Complex Interactions Hairpin-bulge contact

13. 17.6Principles for Predicting RNA Secondary Structure • The most likely structure is the most stable structure • Long regions of base pairing are more stable than short regions • GC base pairs are more stable than AU base pairs • Energies are estimated from experiments with synthetic RNA molecules

14. 5’ 3’ • The structure does not have knots • Loops need to contain at least 4 nucleotides Energies are estimated from experiments with synthetic RNA molecules

15. Note: • Many structures are possible • Formation of some loops prevents formation of other loops • The stabilising effect of paired regions is balanced against the destabilising effect of unpaired regions

16. 17.7Circle Plot Sequence is drawn around circumference of circle Arcs connect paired bases Arcs don’t cross (unless pseudoknots formed) The stabilising effect of paired regions is balanced against the destabilising effect of unpaired regions

17. Squiggle plot Circle plot (unless pseudoknots formed)

18. 17.8ANGIS Programs WAG (Web Angis GCG) RNA secondary structure e.g. mfold Input file: VapHGRNA Output: VAPHGRNA MFOLD Use Plotfold (from WAG) to display output Save as GIF

21. Lehninger Principles of Biochemistry 3rd Edition Nelson & Cox 17.9Ribozymes Self-cleaving RNA molecules Catalytic activity depends on 2o structure

22. 17.10Regulatory RNA - glmS glmS gene produces enzyme GlmS GlmSRNA is a ribozyme – can cleave itself Ribozyme activity is greatly increased by the product of reaction catalysed by GlmS Product of GlmS enzyme shuts off synthesis of GlmS enzyme

23. Cech (2004) Nature 428:263

24. 17.11Regulatory RNAs – csrA, csrB CsrA protein binds to specific mRNAs and prevents their translation CsrB RNA is an antagonist of CsrA - has 18 binding sites for CsrA protein CsrA protein binds to CsrB and is not available to bind to the specific mRNAs

25. Romeo 1998 Mol. Microbiol. 29:1321-1330

26. 5’ 3’ 17.12Evolutionary Relationships RNA homologues maintain secondary structure - covariation of paired bases A U

27. Analysis of sequences of homologues for covariation can be used to predict secondary structure

28. 17.13 Summary Types of secondary structure Principles for prediction of secondary structure mfold program Circle and squiggle plots Secondary structure of regulatory RNA molecules Covariation of paired bases in evolution