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Analysis of tetra- and hepta-nucleotides motifs promoting -1 ribosomal frameshifting in Escherichia coli
Sharma, Virag; Prère, Marie-Francoise; Canal, Isabelle; Firth, Andrew E.; Atkins, John F.; Baranov, Pavel V.; Fayet, Olivier
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.
Keyword(s): Site transfer RNA; Messenger RNA; Gene expression; Translational control; Prokaryotic genomes; Mutational analysis; Bacterial genes; Coding regions; P site; Sequence
Publication Date:
2014
Type: Journal article
Peer-Reviewed: Yes
Language(s): English
Institution: University College Cork
Funder(s): Science Foundation Ireland
Citation(s): Sharma, V., Prère, M.-F., Canal, I., Firth, A. E., Atkins, J. F., Baranov, P. V. and Fayet, O. (2014) 'Analysis of tetra- and hepta-nucleotides motifs promoting -1 ribosomal frameshifting in Escherichia coli', Nucleic Acids Research, 42(11), pp. 7210-7225. doi: 10.1093/nar/gku386
Publisher(s): Oxford University Press
File Format(s): application/pdf
Related Link(s): https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gku386
First Indexed: 2017-11-15 06:30:10 Last Updated: 2017-11-21 06:30:48