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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jul 17, 2017 |
| Title |
Profiling Ssb-Nascent Chain Interactions Reveals Principles of Hsp70-Assisted Folding |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Other
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| Summary |
The yeast Hsp70 chaperone Ssb interacts with ribosomes and nascent chains to co-translationally assist protein folding. Here, we present a proteome-wide analysis of Hsp70 function during translation, based on in vivo selective ribosome profiling, that reveals mechanistic principles coordinating translation with chaperone-assisted protein folding. Ssb binds most cytosolic, nuclear, and mitochondrial proteins and a subset of ER proteins, supporting its general chaperone function. Position-resolved analysis of Ssb engagement reveals compartment- and protein-specific nascent chain binding profiles that are coordinated by emergence of positively charged peptide stretches enriched in aromatic amino acids. Ssbs’ function is temporally coordinated by RAC but independent from NAC. Analysis of ribosome footprint densities along orfs reveals that ribosomes translate faster at times of Ssb binding. This is coordinated by biases in mRNA secondary structure, and codon usage as well as the action of Ssb, suggesting chaperones may allow higher protein synthesis rates by actively coordinating protein synthesis with co-translational folding.
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| Overall design |
Investigating the interaction of Ssb1 and Ssb2 with nascent polypeptide chains in four different strain backgrounds (WT, ssb1/2∆, RAC∆, NAC∆) and the translation speed in WT and ssb1∆ssb2 cells (all in replicates).
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| Contributor(s) |
Döring K, Ahmed N, Riemer T, Suresh HG, Vainsthein Y, Habich M, Riemer J, Mayer MP, O'Brien EP, Kramer G, Bukau B |
| Citation(s) |
28708998, 30158700 |
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| Submission date |
Jan 19, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Kristina Döring |
| E-mail(s) |
[email protected]
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| Organization name |
Heidelberg University
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| Department |
ZMBH
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| Lab |
Bernd Bukau
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| Street address |
Im Neuenheimer Feld 282
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| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
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| Platforms (1) |
| GPL13821 |
Illumina HiSeq 2000 (Saccharomyces cerevisiae) |
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| Samples (40)
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| GSM2463178 |
ssb2∆ Ssb1 interactome, low salt, replicate 1 |
| GSM2463179 |
ssb2∆ Ssb1 interactome, high salt, replicate 1 |
| GSM2463180 |
ssb2∆ Ssb1-GFP translatome, replicate 1 |
| GSM2463181 |
ssb1∆ Ssb2 interactome, low salt, replicate 1 |
| GSM2463182 |
ssb1∆ Ssb2 interactome, high salt, replicate 1 |
| GSM2463183 |
ssb1∆ Ssb2-GFP translatome, replicate 1 |
| GSM2463184 |
ssb2∆ Ssb1 interactome, low salt, replicate 2 |
| GSM2463185 |
ssb2∆ Ssb1 interactome, high salt, replicate 2 |
| GSM2463186 |
ssb2∆ Ssb1-GFP translatome, replicate 2 |
| GSM2463187 |
ssb1∆ Ssb2 interactome, low salt, replicate 2 |
| GSM2463188 |
ssb1∆ Ssb2 interactome, high salt, replicate 2 |
| GSM2463189 |
ssb1∆ Ssb2-GFP translatome, replicate 2 |
| GSM2463190 |
WT Ssb1-GFP translatome, replicate 1 |
| GSM2463191 |
WT Ssb2-GFP translatome, replicate 1 |
| GSM2463192 |
WT Ssb1 interactome, replicate 1 |
| GSM2463193 |
WT Ssb2 interactome, replicate 1 |
| GSM2463194 |
NACΔ Ssb1-GFP translatome, replicate 1 |
| GSM2463195 |
NACΔ Ssb2-GFP translatome, replicate 1 |
| GSM2463196 |
NACΔ Ssb1 interactome, replicate 1 |
| GSM2463197 |
NACΔ Ssb2 interactome, replicate 1 |
| GSM2463198 |
RACΔ Ssb1-GFP translatome, replicate 1 |
| GSM2463199 |
RACΔ Ssb2-GFP translatome, replicate 1 |
| GSM2463200 |
RACΔ Ssb1 interactome, replicate 1 |
| GSM2463201 |
RACΔ Ssb2 interactome, replicate 1 |
| GSM2463202 |
WT Ssb1-GFP translatome, replicate 2 |
| GSM2463203 |
WT Ssb2-GFP translatome, replicate 2 |
| GSM2463204 |
WT Ssb1 interactome, replicate 2 |
| GSM2463205 |
WT Ssb2 interactome, replicate 2 |
| GSM2463206 |
NACΔ Ssb1-GFP translatome, replicate 2 |
| GSM2463207 |
NACΔ Ssb2-GFP translatome, replicate 2 |
| GSM2463208 |
NACΔ Ssb1 interactome, replicate 2 |
| GSM2463209 |
NACΔ Ssb2 interactome, replicate 2 |
| GSM2463210 |
RACΔ Ssb1-GFP translatome, replicate 2 |
| GSM2463211 |
RACΔ Ssb2-GFP translatome, replicate 2 |
| GSM2463212 |
RACΔ Ssb1 interactome, replicate 2 |
| GSM2463213 |
RACΔ Ssb2 interactome, replicate 2 |
| GSM2463214 |
WT translatome, replicate 1 |
| GSM2463215 |
WT translatome, replicate 2 |
| GSM2463216 |
ssb1Δssb2Δ translatome, replicate 1 |
| GSM2463217 |
ssb1Δssb2Δ translatome, replicate 2 |
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| Relations |
| BioProject |
PRJNA362545 |
| SRA |
SRP097127 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE93830_RAW.tar |
2.7 Gb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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