Increased ribosome density associated to positively charged residues is evident in ribosome profiling experiments performed in the absence of translation inhibitors
Rodrigo D. Requião,Henrique José Araujo de Souza,Silvana Rossetto,Tatiana Domitrovic,Fernando L. Palhano +4 more
TLDR
It is concluded that cycloheximide and anisomycin must be avoided in ribosome profiling experiments, as this work showed that reduced translation efficiency associated with polybasic protein sequences could be inferred from ribosom profiling.Abstract:
It has been proposed that polybasic peptides cause slower movement of ribosomes through an electrostatic interaction with the highly negative ribosome exit tunnel. Ribosome profiling data—the sequencing of short ribosome-bound fragments of mRNA—is a powerful tool for the analysis of mRNA translation. Using the yeast Saccharomyces cerevisiae as a model, we showed that reduced translation efficiency associated with polybasic protein sequences could be inferred from ribosome profiling. However, an increase in ribosome density at polybasic sequences was evident only when the commonly used translational inhibitors cycloheximide and anisomycin were omitted during mRNA isolation. Since ribosome profiling performed without inhibitors agrees with experimental evidence obtained by other methods, we conclude that cycloheximide and anisomycin must be avoided in ribosome profiling experiments.read more
Citations
More filters
Journal ArticleDOI
Ribosomal Stalling During Translation: Providing Substrates for Ribosome-Associated Protein Quality Control.
TL;DR: The Ribosomal stalling and rescue steps upstream of the RQCc are reviewed, where one witnesses intersection with cellular machineries implicated in translation elongation, translation termination, ribosomal subunit recycling, and mRNA quality control.
Journal ArticleDOI
Insights into the mechanisms of eukaryotic translation gained with ribosome profiling.
Dmitry E. Andreev,Patrick B F O'Connor,Gary Loughran,Sergey E. Dmitriev,Pavel V. Baranov,Ivan N. Shatsky +5 more
TL;DR: This review will focus on how recent findings made with RiboSeq have revealed important details of the molecular mechanisms of translation in eukaryotes.
Journal ArticleDOI
Asc1, Hel2, and Slh1 couple translation arrest to nascent chain degradation.
TL;DR: It is proposed that Asc1, Hel2, and Slh1 target arresting ribosomes and that this targeting event is a precondition for the RQC to engage the incomplete nascent chain and facilitate its degradation.
Journal ArticleDOI
Role of mRNA structure in the control of protein folding
TL;DR: A model in which the mRNA structure, particularly exceptionally stable RNA structural elements, act as gauges of protein co-translational folding by reducing ribosome speed when the nascent peptide needs time to form and optimize the core structure is suggested.
Journal ArticleDOI
Translation of poly(A) tails leads to precise mRNA cleavage.
Nicholas R. Guydosh,Rachel Green +1 more
TL;DR: This results suggest this process may be critical when changes in the polyadenylation site occur during development, tumorigenesis, or when translation termination/recycling is impaired.
References
More filters
Journal ArticleDOI
Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling
TL;DR: A ribosomesome-profiling strategy based on the deep sequencing of ribosome-protected mRNA fragments is presented and enables genome-wide investigation of translation with subcodon resolution and is used to monitor translation in budding yeast under both rich and starvation conditions.
Journal ArticleDOI
Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes
TL;DR: A suite of techniques, based on ribosome profiling, are presented to provide genome-wide maps of protein synthesis as well as a pulse-chase strategy for determining rates of translation elongation, revealing an unanticipated complexity to mammalian proteomes.
Journal ArticleDOI
The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments.
Nicholas T. Ingolia,Gloria A. Brar,Gloria A. Brar,Silvia Rouskin,Silvia Rouskin,Anna M McGeachy,Anna M McGeachy,Jonathan S. Weissman,Jonathan S. Weissman +8 more
TL;DR: An adaptation that reveals the sites of translation initiation by pretreating cells with harringtonine to immobilize initiating ribosomes is described, paving the way for genome-wide, quantitative analysis of in vivo translation by deep sequencing.
Journal ArticleDOI
An evolutionarily conserved mechanism for controlling the efficiency of protein translation.
Tamir Tuller,Asaf Carmi,Kalin Vestsigian,Sivan Navon,Yuval Dorfan,John M. Zaborske,Tao Pan,Orna Dahan,Itay Furman,Yitzhak Pilpel +9 more
TL;DR: It is suggested that the slow "ramp" at the beginning of mRNAs serves as a late stage of translation initiation, forming an optimal and robust means to reduce ribosomal traffic jams, thus minimizing the cost of protein expression.
Journal ArticleDOI
A Ribosome-Bound Quality Control Complex Triggers Degradation of Nascent Peptides and Signals Translation Stress
Onn Brandman,Jacob Stewart-Ornstein,Daisy Wong,Adam G. Larson,Christopher C. Williams,Gene-Wei Li,Sharleen Zhou,David S. King,Peter S. Shen,Jimena Weibezahn,Joshua G. Dunn,Silvi Rouskin,Toshifumi Inada,Adam Frost,Jonathan S. Weissman +14 more
TL;DR: The range of stresses Hsf1 monitors and elucidates a conserved cotranslational protein quality control mechanism is revealed and the RQC forms a stable complex with 60S ribosomal subunits containing stalled polypeptides and triggers their degradation.