Ribosome profiling analysis of eEF3-depleted Saccharomyces cerevisiae
Kasari, Villu ; Margus, Tõnu ; Atkinson, Gemma C. LU ; Johansson, Marcus J.O. LU and Hauryliuk, Vasili LU
(2019)
In Scientific Reports
9.
p.1-10
- Abstract
In addition to the standard set of translation factors common in eukaryotic organisms, protein synthesis in the yeast Saccharomyces cerevisiae requires an ABCF ATPase factor eEF3, eukaryotic Elongation Factor 3. eEF3 is an E-site binder that was originally identified as an essential factor involved in the elongation stage of protein synthesis. Recent biochemical experiments suggest an additional function of eEF3 in ribosome recycling. We have characterised the global effects of eEF3 depletion on translation using ribosome profiling. Depletion of eEF3 results in decreased ribosome density at the stop codon, indicating that ribosome recycling does not become rate limiting when eEF3 levels are low. Consistent with a defect in translation... (More)
In addition to the standard set of translation factors common in eukaryotic organisms, protein synthesis in the yeast Saccharomyces cerevisiae requires an ABCF ATPase factor eEF3, eukaryotic Elongation Factor 3. eEF3 is an E-site binder that was originally identified as an essential factor involved in the elongation stage of protein synthesis. Recent biochemical experiments suggest an additional function of eEF3 in ribosome recycling. We have characterised the global effects of eEF3 depletion on translation using ribosome profiling. Depletion of eEF3 results in decreased ribosome density at the stop codon, indicating that ribosome recycling does not become rate limiting when eEF3 levels are low. Consistent with a defect in translation elongation, eEF3 depletion causes a moderate redistribution of ribosomes towards the 5′ part of the open reading frames. We observed no E-site codon- or amino acid-specific ribosome stalling upon eEF3 depletion, supporting its role as a general elongation factor. Surprisingly, depletion of eEF3 leads to a relative decrease in P-site proline stalling, which we hypothesise is a secondary effect of generally decreased translation and/or decreased competition for the E-site with eIF5A.
(Less)
- author
- Kasari, Villu
; Margus, Tõnu
; Atkinson, Gemma C.
LU
; Johansson, Marcus J.O.
LU
and Hauryliuk, Vasili
LU
- publishing date
- 2019
- type
- Contribution to journal
- publication status
- published
- in
- Scientific Reports
- volume
- 9
- article number
- 3037
- pages
- 1 - 10
- publisher
- Nature Publishing Group
- external identifiers
-
- pmid:30816176
- scopus:85062273271
- ISSN
- 2045-2322
- DOI
- 10.1038/s41598-019-39403-y
- language
- English
- LU publication?
- no
- additional info
- Funding Information: We are grateful to Akira Kaji for sharing anti-eEF3 antibodies and Nicholas Ingolia for sharing protocols for Ribo-Seq library preparation and help with data analysis. This work was supported by the funds from European Regional Development Fund through the Centre of Excellence for Molecular Cell Technology (V.H.); the Molecular Infection Medicine Sweden (MIMS) (V.H.); Swedish Research council (grant 2017-03783 to VH, 2015- 04746 to GCA); Ragnar Söderberg foundation (V.H.); Magnus Bergvalls Foundation (2017-02098 to M.J.); Åke Wibergs Foundation (M14-0207 to M.J.); and Kempestiftelsernas grants (JCK-1627 to GCA and SMK-1349 to V.H.). Publisher Copyright: © 2019, The Author(s). Copyright: Copyright 2019 Elsevier B.V., All rights reserved.
- id
- 93dd214f-9cf2-4c10-9cff-f65210aea525
- date added to LUP
- 2021-09-24 20:35:59
- date last changed
- 2024-04-20 12:55:20
@article{93dd214f-9cf2-4c10-9cff-f65210aea525,
abstract = {{<p>In addition to the standard set of translation factors common in eukaryotic organisms, protein synthesis in the yeast Saccharomyces cerevisiae requires an ABCF ATPase factor eEF3, eukaryotic Elongation Factor 3. eEF3 is an E-site binder that was originally identified as an essential factor involved in the elongation stage of protein synthesis. Recent biochemical experiments suggest an additional function of eEF3 in ribosome recycling. We have characterised the global effects of eEF3 depletion on translation using ribosome profiling. Depletion of eEF3 results in decreased ribosome density at the stop codon, indicating that ribosome recycling does not become rate limiting when eEF3 levels are low. Consistent with a defect in translation elongation, eEF3 depletion causes a moderate redistribution of ribosomes towards the 5′ part of the open reading frames. We observed no E-site codon- or amino acid-specific ribosome stalling upon eEF3 depletion, supporting its role as a general elongation factor. Surprisingly, depletion of eEF3 leads to a relative decrease in P-site proline stalling, which we hypothesise is a secondary effect of generally decreased translation and/or decreased competition for the E-site with eIF5A.</p>}},
author = {{Kasari, Villu and Margus, Tõnu and Atkinson, Gemma C. and Johansson, Marcus J.O. and Hauryliuk, Vasili}},
issn = {{2045-2322}},
language = {{eng}},
pages = {{1--10}},
publisher = {{Nature Publishing Group}},
series = {{Scientific Reports}},
title = {{Ribosome profiling analysis of eEF3-depleted Saccharomyces cerevisiae}},
url = {{http://dx.doi.org/10.1038/s41598-019-39403-y}},
doi = {{10.1038/s41598-019-39403-y}},
volume = {{9}},
year = {{2019}},
}