Analysis of tetra- and hepta-nucleotides motifs promoting -1 ribosomal frameshifting in Escherichia coli |
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| Authors: | Virag Sharma Marie-Fran?oise Prère Isabelle Canal Andrew E. Firth John F. Atkins Pavel V. Baranov Olivier Fayet |
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| Affiliation: | 1.School of Biochemistry and Cell biology, University College Cork, Cork, Ireland;2.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;3.Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK;4.Department of Human Genetics, University of Utah, 15N 2030E, Rm7410, Salt Lake City, UT 84112-5330, USA |
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| 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. |
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