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The Effect of the URM1 Pathway on Translation by Thiolation of Specific Trnas

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The Effect of the URM1 Pathway on Translation by Thiolation of Specific Trnas Research Collection Doctoral Thesis The effect of the URM1 pathway on translation by thiolation of specific tRNAs Author(s): Rezgui, Vanessa Anissa Nathalie Publication Date: 2012 Permanent Link: https://doi.org/10.3929/ethz-a-007624233 Rights / License: In Copyright - Non-Commercial Use Permitted This page was generated automatically upon download from the ETH Zurich Research Collection. For more information please consult the Terms of use. ETH Library DISS. ETH NO. 20870 The effect of the URM1 pathway on translation by thiolation of specific tRNAs A dissertation submitted to ETH ZURICH for the degree of Doctor of Sciences presented by Vanessa Anissa Nathalie Rezgui M.Sc. University of Geneva born on April, 28th 1981 citizen of Switzerland (Zurich) accepted on the recommendation of Prof. Matthias Peter – examiner Prof. André Gerber – co-examiner Prof. Paola Picotti – co-examiner 2012 TABLE OF CONTENTS SUMMARY ........................................................................................................ 4 RESUMÉ ............................................................................................................ 5 1 Introduction. ............................................................................................... 6 1.1 Translation............................................................................................................................................ 6 1.2 Translation regulation....................................................................................................................... 7 1.3 Regulation of tRNAs ........................................................................................................................ 8 1.3.1 tRNA abundance...........................................................................................................................9 1.3.2 tRNA aminoacylation levels.................................................................................................. 11 1.3.3 tRNA localization ...................................................................................................................... 11 1.4 tRNA modifications ........................................................................................................................11 1.4.1 Wobble base modifications ................................................................................................... 13 1.4.2 The mcm5s2U34 modification................................................................................................. 14 1.5 The Ubiquitin-related modifier 1................................................................................................16 1.6 Phenotypes associated with lack of wobble uridine modification...................................17 1.7 Aim of the work................................................................................................................................19 2 RESULTS......................................................................................................20 2.1 General translation is unaffected by lack of URM1 .............................................................20 2.2 URM1 is important for efficient expression of AAA, CAA, and GAA-rich proteins 23 2.3 Differential expression of AAA, CAA, and GAA-rich genes is not due to differential transcription.........................................................................................................................................................28 2.4 The protein expression changes induced by lack of URM1 are small............................30 2.5 URM1 is required for efficient translation of CMS1 and YPL199C................................31 2.6 Thiolation is required for codon-specific translation...........................................................33 2.6.1 Generation of an inducible dual-fluorescent reporter .............................................. 33 2.6.2 URM1 is required for expression of AAA, CAA, and GAA enriched reporters... 36 2.6.3 Reporters with the G-ending codons are less affected by lack of thiolation.... 39 2.6.4 The effect of URM1 on translation is dependent on codon frequency................ 41 2.6.5 Addition of various drugs does not increase the urm1∆ effect on the translation reporters..................................................................................................................................... 41 2.7 Thiolation enhances A-site binding and peptide bond formation....................................44 2.8 URM1-deleted cells are sensitive to paromomycin ..............................................................47 1 2.9 Activation of galactose promoter is defective in urm1∆ cells ..........................................48 3 DISCUSSION................................................................................................51 3.1 Uracil34 modifications stabilizes tRNAs at the A-site .....................................................51 3.2 Consequences on translation fidelity....................................................................................51 3.3 Effects of lack of thiolation on expression of AAA, CAA, and GAA rich mRNAs.52 3.4 Effects of lack of thiolation on expression of AAG, CAG, and GAG rich proteins .53 3.5 Codon context ...................................................................................................................................54 3.6 The role of URM1 in rich conditions.........................................................................................55 3.7 URM1 involvement in stress regulation ...................................................................................55 3.7.1 Thiolation and tRNA levels.................................................................................................... 55 3.7.2 Regulation of tRNA modification levels........................................................................... 57 3.8 Influence of tRNA modifications on each other....................................................................58 3.9 Identification of further reGulated proteins.......................................................................59 3.10 Functions of tRNA modifications beyond translation.......................................................60 3.11 Other functions of Urm1.............................................................................................................61 3.12 Concluding remarks......................................................................................................................62 4 Materials and Methods...............................................................................64 4.1 [35S] metabolic labeling..................................................................................................................64 4.2 Ribosome extraction .......................................................................................................................64 4.3 Polysome profiles.............................................................................................................................65 4.4 Hot phenol extraction .....................................................................................................................65 4.5 Gene ontology (GO) enrichment analysis ...............................................................................65 4.6 Quantitative RT-PCR .....................................................................................................................66 4.7 Cloning of the dual-fluorescent translation reporter ............................................................66 4.8 Expression of fluorescent reporter .............................................................................................66 4.9 Cycloheximide chase......................................................................................................................67 4.10 Western blotting.............................................................................................................................67 4.11 Galactose induction.......................................................................................................................67 4.12 Drug sensitivity assay ..................................................................................................................67 4.13 SILAC labelinG...............................................................................................................................68 4.14 Protein Extraction and diGestion for MS...........................................................................68 4.15 Strong cation exchange (SCX) fractionation....................................................................68 4.16 Peptide purification and iso-electric focusinG................................................................68 4.17 LC-MS/MS.......................................................................................................................................69 4.18 Protein identification and quantitation.............................................................................69 2 4.19 Data normalization and statistical analysis of differential abundance................70 4.20 Random Forrest Analysis ........................................................................................................70 4.21 Total tRNA preparation............................................................................................................70 4.22 Lysine tRNA synthetase cloning and purification.........................................................71
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