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A genome-wide perspective on translation of proteins

A genome-wide perspective on translation of proteins. Dec 2012 Regulatory Genomics Lecturer: Prof. Yitzhak Pilpel. Multiple codons for the same amino acid: opportunities for sophisticated control. C1 C2 C3 C4 C5 C6 Serine: UCU UCC UCA UCG AGC AGU Cysteine: UGU UGC

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A genome-wide perspective on translation of proteins

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

  2. Multiple codons for the same amino acid: opportunities for sophisticated control C1 C2 C3 C4 C5 C6 Serine: UCU UCC UCA UCG AGC AGU Cysteine: UGU UGC Methionine: UGG STOP: UAA, UAG UGA

  3. Wobble Interaction { Wi/Wmaxif Wi0 wi = wmeanelse ATC CCA AAA TCG AAT A simple model for translation efficiency … … … The tRNA Adaptation Index (tAI) dos Reis et al. NAR 2004

  4. Codon usage bias is correlated with translation efficiency r=-0.79 (p<0.001) Mutation pattern (neutral) Selection Codon bias

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

  6. Kinetic proofreading – the problem kc vc c + C cC AAc C – codon c – Cognate tRNA d – None-cognate tRNA cC, dC – tRNAcodon pair AAc, AAd, correct and wrong amino acid Assumptions: kc=kd, k’d=100*k’c vd=vc k’c + d k’d kd dC vd AAd Error rate, Fo= AAd/AAc = dC/cC = k’c/k;d= 0.01 Yet in reality error rate is 10^-4… How can we explain 100 times more accurate translation

  7. Kinetic proofreading – the solution l’c kc vc m c + C cC AAc c*C k’c + C – codon C* – Modified Cognate tRNA d* – Modified None-cognate tRNA C*C, d*C – tRNAcodon pair m- rate of tRNAmodification l’c, l’d – rate of unidirectional reaction in which the modified tRNAs leave the site Assumption: l’c*100=l’d d l’d k’d kd dC m d*C vd Corrected Error rate, F= (k’c/k’d) (l’c/l’d)= 10^-4 AAd

  8. 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 C

  9. Analogy: from mating in yeast A protease might help yeast find the right mate by degrading the signal and the noise No protease: large error With protease: small error Barkai et al. Nature 1998

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

  11. Programmed “errors” in amino acid loading on tRNA in stress Oxygen radicals – toxic !!! A non-Met tRNA As a result, in times of oxidative stress the cell is more protected since it has more Met residues in its proteins !! (Netzer et al Nature 2009)

  12. Open questions • Does select act to tune the “desired” error rate? • How can we find places in genes where high error rate is selected for/against? • Does controlling tRNA availability serve as a means to control error rate? • Are there additional factors (e.g. location of codon within a gene)?

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

  14. Wobble Interaction { Wi/Wmaxif Wi0 wi = wmeanelse ATC CCA AAA TCG AAT A simple model for translation efficiency … … … The tRNA Adaptation Index (tAI) dos Reis et al. NAR 2004

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

  16. Yet, mRNA also correlates with tAI… and with protein levels… mRNA * * * * * * * tAI

  17. tAI and protein levels correlate even among gene populations with same mRNA levels

  18. Deletion of a gene with a duplicate has smaller effect on phenotype (Gu et al Nature 2002) • Single-copy genes have a tendency to be essential • Genes with duplicates tend to be more dispensable

  19. As always, correlation doesn’t guarantee causality Duplication Dispensability Z(??)

  20. A synthetic library of GFP variants Kudla et al. Science 2009

  21. No correlation between CAI and protein expression Protein abundance

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

  23. Tight RNA structure reduce translation Protein abundance

  24. The tightness at the 5’ matters

  25. So if codon usage doesn’t affect protein level, what does effect such levels? – It’s the RNA structure and its tightness!

  26. Is tightness important throughout, or just at particular locations? ?

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

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

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

  30. No correlation between CAI and protein expression Protein abundance

  31. Towards more sophisticated translation efficiency models

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