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Sci Rep. 2019 Feb 28;9(1):3037. doi: 10.1038/s41598-019-39403-y.

Ribosome profiling analysis of eEF3-depleted Saccharomyces cerevisiae.

Author information

1
Department of Molecular Biology, Umeå University, SE-901 87, Umeå, Sweden.
2
Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-901 87, Umeå, Sweden.
3
Department of Molecular Biology, Umeå University, SE-901 87, Umeå, Sweden. gemma.atkinson@umu.se.
4
Department of Molecular Biology, Umeå University, SE-901 87, Umeå, Sweden. marcus.johansson@umu.se.
5
Department of Molecular Biology, Umeå University, SE-901 87, Umeå, Sweden. vasili.hauryliuk@umu.se.
6
Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-901 87, Umeå, Sweden. vasili.hauryliuk@umu.se.
7
University of Tartu, Institute of Technology, 50411, Tartu, Estonia. vasili.hauryliuk@umu.se.

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 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.

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