Nedialkova et al. 2015 (PRJNA279785)
General Details
| Title | Optimization of codon translation rates via tRNA modifications maintains proteome integrity |
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| Organism | |
| Number of Samples | 70 |
| Release Date | 2015/03/28 00:00 |
| Sequencing Types | |
| Protocol Details |
Study Links
| GWIPS-viz | Trips-Viz |
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| Visit GWIPS-viz | Visit Trips-Viz |
Repository Details
| SRA | SRP056647 |
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| ENA | SRP056647 |
| GEO | GSE67387 |
| BioProject | PRJNA279785 |
Publication
| Title | |
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| Authors | Nedialkova DD,Leidel SA |
| Journal | Cell |
| Publication Date | 2015 Jun 18 |
| Abstract | Proteins begin to fold as they emerge from translating ribosomes. The kinetics of ribosome transit along a given mRNA can influence nascent chain folding, but the extent to which individual codon translation rates impact proteome integrity remains unknown. Here, we show that slower decoding of discrete codons elicits widespread protein aggregation in vivo. Using ribosome profiling, we find that loss of anticodon wobble uridine (U34) modifications in a subset of tRNAs leads to ribosome pausing at their cognate codons in S. cerevisiae and C. elegans. Cells lacking U34 modifications exhibit gene expression hallmarks of proteotoxic stress, accumulate aggregates of endogenous proteins, and are severely compromised in clearing stress-induced protein aggregates. Overexpression of hypomodified tRNAs alleviates ribosome pausing, concomitantly restoring protein homeostasis. Our findings demonstrate that modified U34 is an evolutionarily conserved accelerator of decoding and reveal an unanticipated role for tRNA modifications in maintaining proteome integrity. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved. |
| PMC | PMC4503807 |
| PMID | 26052047 |
| DOI |
| Run Accession | Study Accession | Scientific Name | Cell Line | Library Type | Treatment | GWIPS-viz | Trips-Viz | Reads | BAM | BigWig (F) | BigWig (R) | ||
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| SRR1944940 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide |  |
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| SRR1944941 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1944912 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1944913 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1944914 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1944915 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1944916 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1944917 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1944918 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1944919 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1944920 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1944921 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1944922 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1944923 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1944936 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1944937 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1944938 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1944939 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1944948 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1944949 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1944950 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1944951 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1944952 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1944953 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1944960 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1944961 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1944962 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1944963 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1944964 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1944965 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1944966 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1944967 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1944968 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1944969 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1944970 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1944971 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1944972 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1944973 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1944974 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1944975 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1944976 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1944977 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1944978 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1944979 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1944980 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1944981 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Frozen | |
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| SRR1944982 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Frozen | |
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| SRR1944983 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Frozen | |
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| SRR1944984 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Frozen | |
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| SRR1944985 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Frozen | |
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| SRR1944986 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Frozen | |
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| SRR1944987 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1944988 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1944989 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1944990 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1944991 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1944992 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1944993 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1944994 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1944995 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1944996 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1944997 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1944998 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1944999 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1945000 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1945001 | PRJNA279785 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1945002 | PRJNA279785 | Caenorhabditis elegans | Ribo-Seq |  |
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| SRR1945003 | PRJNA279785 | Caenorhabditis elegans | Ribo-Seq | |
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| SRR1945004 | PRJNA279785 | Caenorhabditis elegans | Ribo-Seq | |
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| SRR1945005 | PRJNA279785 | Caenorhabditis elegans | Ribo-Seq | |
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| Run Accession | Study Accession | Scientific Name | Cell Line | Library Type | Treatment | GWIPS-viz | Trips-Viz | Reads | BAM | BigWig (F) | BigWig (R) |
ⓘ For more Information on the columns shown here see: About