title: Increased ribosome density associated to positively charged residues is evident in ribosome profiling experiments performed in the absence of translation inhibitors.
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.
authors.affiliation: a Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro , Rio de Janeiro , RJ , Brazil.
authors.forename: Rodrigo D
authors.initials: RD
authors.lastname: Requião
authors.affiliation: b Programa de Pós-Graduação em Informática, Universidade Federal do Rio de Janeiro , Rio de Janeiro , RJ , Brazil.
authors.forename: Henrique José Araujo
authors.initials: HJ
authors.lastname: de Souza
authors.affiliation: b Programa de Pós-Graduação em Informática, Universidade Federal do Rio de Janeiro , Rio de Janeiro , RJ , Brazil.
authors.forename: Silvana
authors.initials: S
authors.lastname: Rossetto
authors.affiliation: c Departamento de Virologia , Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro , Rio de Janeiro , Brazil.
authors.forename: Tatiana
authors.initials: T
authors.lastname: Domitrovic
authors.affiliation: a Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro , Rio de Janeiro , RJ , Brazil.
authors.forename: Fernando L
authors.initials: FL
authors.lastname: Palhano
mesh_terms: D014176:Protein Biosynthesis; D011500:Protein Synthesis Inhibitors / Q000494:pharmacology; D012331:RNA, Fungal / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics* / Q000378:metabolism; D012270:Ribosomes / Q000378:metabolism*; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D011500:Protein Synthesis Inhibitors; D012331:RNA, Fungal; D012333:RNA, Messenger
keywords: Cycloheximide; polyA sequences; polybasic sequences; ribosome profiling; ribosome translation