A genome-wide perspective on translation of proteins

1. A genome-wide perspective on translation of proteins Jan 2012 Regulatory Genomics Lecturer: Prof. Yitzhak Pilpel

2. Selection of codons might affect: Accuracy Throughput RNA-structure Costs Folding

3. The energy landscape of kinetic proofreading l’c d*C l’d c*C Free energy c d C k’d dC k’c cC Fo d c C F=Fo* C

4. Selection of codons might affect: Accuracy Throughput RNA-structure Costs Folding

5. No correlation between CAI and protein expression among synthetic genes Protein abundance

6. Correlation does not imply causality!! r=0.63 Measured protein abundance Physiological Evolutionary Predicted translation efficiency (Ghaemmaghami et al. Nature 2003)

7. Tight RNA structure reduce translation Protein abundance

8. The tightness at the 5’ matters

9. Natural sequences too show relaxed structure at 5’ (Tuller PNAS 2010) Structural tightness Structural tightness

10. Yet, mRNA structure doesn’t predict expression at all Protein/mRNA Structural Tightness

11. Bioinformatics vs. synthetic biology Bioinformatics Synthetic biology Variability is controlled (few confounding factors) Hundreds of thousands of genes All passed through natural selection

12. Maybe we had a wrong (i.e. too simple) model for evaluating effect of codons on TE?

13. Multiple ribosomes may translate the same message simultaneously

14. A genome-wide method to measure translation efficiency (Ingolia Science 2009)

15. Translational response to starvation

16. Putative new ORFs in viruses How do we validate the new predictions? What does it mean to “validate” such predictions??

17. A genome-wide density profile of ribosomes in yeast Ingolia et al. Nature 2009

18. Low initial ramp is conserved in evolution Availability of tRNA Tuller Cell 2010

19. Ribosomal density is explained by computed speed 5’ -> 3’ Fluxi,i+1 = vi*Ji Fluxi,i+1 = Fluxi+1,i+2 At steady-state 1/vi=Ji

20. Selection of codons might affect: Accuracy Throughput RNA-structure Costs Folding

21. CAA CAG AAA TCG AAT Hypothesis: Traffic control by availability of raw material …

22. The anti-Shine–Dalgarno sequence drives translational pausing and codon choice in bacteriaGene-Wei Li, Eugene Oh & Jonathan S. Weissman System Biology Retreat 2012

23. Abstract a genome-wide analysis of pausing in bacteria by ribosome profiling. codons decoded by rare tRNAs do not lead to slow translation under nutrient-rich conditions. Shine–Dalgarno(SD) like features cause translational pausing. pausing is due to hybridization between the mRNA and 16S rRNA of the translating ribosome. In protein-coding sequences, internal SD sequences are disfavoured. SD-like sequences are a major determinant of translation rates and a global driving force for the coding of bacterial genomes.

24. Ribosome Profiling Per transcript • Ribosomes protect from • Micrococcal Nuclease

25. Motivation ribosome occupancy is highly variable across coding regions ribosome density often surpasses by more than tenfold the mean density Most pauses are uncharacterized.  Where do the pausing come from???

26. Pausing due to codons usage? NO!* LB medium Serine codons • Why Serine? • serine is the first amino acid to be catabolized by E. coli when sugar is absent • the increased ribosome occupancy might be due to limited serine supply. glucose-supplemented MOPS medium  the identity of the A-site codon could not account for the large variability in ribosome density along messages

27. Pausing are due to Shine–Dalgarno (SD) like features • Codons resemble features in the SD (AGGAGGU in E. coli) • coincides with spacing for ribosome binding sites.

28. Pausing are due to SD-like features

29. Is it Elongating or Initiating Ribosomes? Experiment: Create a cell with: WT-ribosomes, O-ribosome & oSD-lacZ. • On oSD-lacZ: • Pausing on SD-like  initiation (by WT ribosomes) • NO Pausing on SD-like  elongating ribosomes

30. Pausing are of Elongating Ribosomes SD-lacZ SD-lacZ oSD-lacZ Other Genes Other Genes SD-like oSD-like oSD-lacZ SD-like oSD-like

31. Internal SD sequences are disfavoured strong SD-like sequences are generally avoided in the coding region

32. SD-like features affect codon selection GAG, AGG, and GGG are all minor codons Selection against two consecutive codons that resemble SD sequences

33. Why pause ribosomes??

34. Correspondence of protein structure and ribosome pausing

35. Conclusions and Discussions • SD-like features explain pausings, not codons • SD-like features & 16S elongating ribosome interacation • SD-like sequneces are disfavored  to optimiaze translation consider peptide sequence • Interactions with ribosomes  SD-like codons are disfavoured tRNA expression. • conserved  pausing can be exploited for functional purposes: • Frameshifting, folding, transcriptional regulation

36. Towards more sophisticated translation efficiency models

37. tRNAs may be recycled … CAA CAG AAA TCG AAT TCG Due to recycling the local concentration of a rare tRNA might be high in a near-by codon

38. Codon Order Influences the Speed of Translation in Yeast Cells Natural genes have a tendency to look like . I.e. if a rare codon appears at a given position it has an elevated tendency to occur again shortly after along the gene Cannarozzi et al Cell 2010

39. Selection of codons might affect: Accuracy Throughput RNA-structure Costs Folding

40. Selection of codons might affect: Accuracy Throughput RNA-structure Costs Folding

41. Slow Fast Rare codons at domain-boundaries may support folding Glu ? GAA (14) GAG (2) Argos et al. Protein Science 1996

42. Transient ribosomal attenuation coordinates protein synthesis and co-translational folding Nature Structural & Molecular Biology 16, 274 - 280 (2009)

43. Due to co-translation-folding a “synonymous mutation caused a disease – changed a fast codon to a slow one disrupted synchrony of translation and folding