title: Ribosomal initiation complexes probed by toeprinting and effect of trans-acting translational regulators in bacteria.
abstract: Toeprinting was developed to study the formation of ribosomal initiation complexes in bacteria. This approach, based on the inhibition of reverse transcriptase elongation, was used to monitor the effect of ribosomal components and translational factors on the formation of the active ribosomal initiation complex. Moreover, this method offers an easy way to study in vitro how mRNA conformational changes alter ribosome binding at the initiation site. These changes can be induced either by environmental cues (temperature, ion concentration), or by the binding of metabolites, regulatory proteins, and trans-acting RNAs. An experimental guide is given to follow the different steps of the formation of ribosomal initiation complexes in Escherichia coli and Staphylococcus aureus, and to monitor the mechanism of action of several regulators on translation initiation in vitro. Protocols to prepare the ribosome and the subunits are also given for Thermus thermophilus, Staphylococcus aureus, and Escherichia coli.
authors.affiliation: Université de Strasbourg, F-67084, Strasbourg, France.
authors.forename: Pierre
authors.initials: P
authors.lastname: Fechter
authors.forename: Clément
authors.initials: C
authors.lastname: Chevalier
authors.forename: Gulnara
authors.initials: G
authors.lastname: Yusupova
authors.forename: Marat
authors.initials: M
authors.lastname: Yusupov
authors.forename: Pascale
authors.initials: P
authors.lastname: Romby
authors.forename: Stefano
authors.initials: S
authors.lastname: Marzi
mesh_terms: D001419:Bacteria / Q000235:genetics* / Q000378:metabolism*; D001426:Bacterial Proteins / Q000378:metabolism*; D001483:Base Sequence; D004926:Escherichia coli / Q000378:metabolism; D008967:Molecular Biology / Q000379:methods*; D008969:Molecular Sequence Data; D010442:Peptide Chain Initiation, Translational; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics; D012270:Ribosomes / Q000378:metabolism*; D013211:Staphylococcus aureus / Q000378:metabolism; D016963:Thermus thermophilus / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D012329:RNA, Bacterial