Ribosome profiling analysis of eEF3-depleted Saccharomyces cerevisiae

Scientific Reports
Villu KasariVasili Hauryliuk

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.

References

Jan 1, 1985·Molecular & General Genetics : MGG·S SangsodaY Surdin-Kerjan
Jul 1, 1988·Journal of Biochemistry·M Uritani, M Miyazaki
Jun 19, 1984·Biochemistry·J S HutchisonK Moldave
Sep 1, 1995·The Journal of Biological Chemistry·F J Triana-AlonsoK H Nierhaus
Feb 1, 1995·Biochemical Society Transactions·N Ross-SmithM F Tuite
Dec 21, 2002·The Journal of Biological Chemistry·Monika AnandTerri Goss Kinzy
Feb 21, 2006·Trends in Biochemical Sciences·Go HirokawaAkira Kaji
Aug 25, 2006·Nature·Christian B F AndersenRoland Beckmann
Sep 30, 2008·Journal of Molecular Biology·Jianli Lu, Carol Deutsch
Jul 14, 2009·Nucleic Acids Research·Peter KötterBeatrix Suess
Aug 25, 2009·Nature·Wenqian HuJeff Coller
Jun 11, 2010·Proceedings of the National Academy of Sciences of the United States of America·Shinya KurataHideko Kaji
Mar 22, 2012·Database : the Journal of Biological Databases and Curation·Rama BalakrishnanJ Michael Cherry
Jun 4, 2013·Molecular Cell·Erik GutierrezThomas E Dever
Oct 8, 2013·Nature Methods·Joseph P O'SheaDaniel Schwartz
Jul 25, 2014·Nucleic Acids Research·Maxim V Gerashchenko, Vadim N Gladyshev
Oct 29, 2014·Proceedings of the National Academy of Sciences of the United States of America·Krishna KannanAlexander S Mankin
Jun 6, 2015·Cell·Vicent PelechanoLars M Steinmetz
Oct 16, 2015·Nature Reviews. Molecular Cell Biology·Gloria A Brar, Jonathan S Weissman
Apr 28, 2016·Wiley Interdisciplinary Reviews. RNA·Clarence Ling, Dmitri N Ermolenko
Aug 26, 2016·Nature Protocols·Mihaela PerteaSteven L Salzberg
Oct 30, 2016·Proceedings of the National Academy of Sciences of the United States of America·James MarksAlexander S Mankin
Dec 8, 2016·Nucleic Acids Research·Dmitry E AndreevIvan N Shatsky
Apr 11, 2017·Molecular Cell·Anthony P SchullerRachel Green
Sep 29, 2018·F1000Research·Steven W Wingett, Simon Andrews

❮ Previous
Next ❯

Citations

Jul 13, 2019·Nucleic Acids Research·Villu KasariVasili Hauryliuk
Jun 25, 2020·Proceedings of the National Academy of Sciences of the United States of America·Aleksandra S AnisimovaVadim N Gladyshev
Jul 30, 2020·MSystems·Adrián López García de LomanaNitin S Baliga
Feb 9, 2021·The EMBO Journal·Namit RanjanDaniel N Wilson
Dec 12, 2020·Nucleic Acids Research·Ofri Levi, Yoav S Arava

❮ Previous
Next ❯

Methods Mentioned

BETA
GTPase
Ribo-Seq
RNA-Seq
PCR

Software Mentioned

Ribo
Python
Cutadapt
YeastMine Gene Ontology ( GO )
FastQC
pLogo

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.