title: Analysis of tetra- and hepta-nucleotides motifs promoting -1 ribosomal frameshifting in Escherichia coli.
abstract: Programmed ribosomal -1 frameshifting is a non-standard decoding process occurring when ribosomes encounter a signal embedded in the mRNA of certain eukaryotic and prokaryotic genes. This signal has a mandatory component, the frameshift motif: it is either a Z_ZZN tetramer or a X_XXZ_ZZN heptamer (where ZZZ and XXX are three identical nucleotides) allowing cognate or near-cognate repairing to the -1 frame of the A site or A and P sites tRNAs. Depending on the signal, the frameshifting frequency can vary over a wide range, from less than 1% to more than 50%. The present study combines experimental and bioinformatics approaches to carry out (i) a systematic analysis of the frameshift propensity of all possible motifs (16 Z_ZZN tetramers and 64 X_XXZ_ZZN heptamers) in Escherichia coli and (ii) the identification of genes potentially using this mode of expression amongst 36 Enterobacteriaceae genomes. While motif efficiency varies widely, a major distinctive rule of bacterial -1 frameshifting is that the most efficient motifs are those allowing cognate re-pairing of the A site tRNA from ZZN to ZZZ. The outcome of the genomic search is a set of 69 gene clusters, 59 of which constitute new candidates for functional utilization of -1 frameshifting.
authors.affiliation: School of Biochemistry and Cell biology, University College Cork, Cork, Ireland.
authors.forename: Virag
authors.initials: V
authors.lastname: Sharma
authors.affiliation: Laboratoire de Microbiologie et Génétique moléculaire, UMR5100, Centre National de la Recherche Scientifique, Université Paul Sabatier-Toulouse III, 118 route de Narbonne, Toulouse 31062-cedex, France.
authors.forename: Marie-Françoise
authors.initials: MF
authors.lastname: Prère
authors.affiliation: Laboratoire de Microbiologie et Génétique moléculaire, UMR5100, Centre National de la Recherche Scientifique, Université Paul Sabatier-Toulouse III, 118 route de Narbonne, Toulouse 31062-cedex, France.
authors.forename: Isabelle
authors.initials: I
authors.lastname: Canal
authors.affiliation: Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK.
authors.forename: Andrew E
authors.initials: AE
authors.lastname: Firth
authors.affiliation: School of Biochemistry and Cell biology, University College Cork, Cork, Ireland Department of Human Genetics, University of Utah, 15N 2030E, Rm7410, Salt Lake City, UT 84112-5330, USA.
authors.forename: John F
authors.initials: JF
authors.lastname: Atkins
authors.affiliation: School of Biochemistry and Cell biology, University College Cork, Cork, Ireland.
authors.forename: Pavel V
authors.initials: PV
authors.lastname: Baranov
authors.affiliation: Laboratoire de Microbiologie et Génétique moléculaire, UMR5100, Centre National de la Recherche Scientifique, Université Paul Sabatier-Toulouse III, 118 route de Narbonne, Toulouse 31062-cedex, France Olivier.Fayet@ibcg.biotoul.fr.
authors.forename: Olivier
authors.initials: O
authors.lastname: Fayet
mesh_terms: D004926:Escherichia coli / Q000235:genetics*; D018965:Frameshifting, Ribosomal; D005798:Genes, Bacterial; D059372:Nucleotide Motifs; D009711:Nucleotides / Q000032:analysis; D012333:RNA, Messenger / Q000737:chemistry*
chemical_list: D009711:Nucleotides; D012333:RNA, Messenger