Analysis of tetra- and hepta-nucleotides motifs promoting -1 ribosomal frameshifting in Escherichia coli

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dc.contributor.authorSharma, Virag
dc.contributor.authorPrère, Marie-Francoise
dc.contributor.authorCanal, Isabelle
dc.contributor.authorFirth, Andrew E.
dc.contributor.authorAtkins, John F.
dc.contributor.authorBaranov, Pavel V.
dc.contributor.authorFayet, Olivier
dc.contributor.funderScience Foundation Ireland
dc.contributor.funderWellcome Trust
dc.contributor.funderAgence Nationale de la Recherche
dc.contributor.funderUniversité Toulouse III - Paul Sabatier
dc.contributor.funderCentre National de la Recherche Scientifique
dc.date.accessioned2017-11-14T13:24:30Z
dc.date.available2017-11-14T13:24:30Z
dc.date.issued2014
dc.description.abstractProgrammed 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.en
dc.description.sponsorshipCentre national de la Recherche Scientifique; Universite Paul Sabatier-Toulouse III; Agence National de la Recherche (NT05 1_44848); Wellcome Trust (094423; 088789); Science Foundation Ireland (R14989)en
dc.description.statusPeer revieweden
dc.description.versionPublished Versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.citationSharma, 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/gku386en
dc.identifier.doi10.1093/nar/gku386
dc.identifier.endpage7225
dc.identifier.issn0305-1048
dc.identifier.issn1362-4962
dc.identifier.issued11
dc.identifier.journaltitleNucleic Acids Researchen
dc.identifier.startpage7210
dc.identifier.urihttps://hdl.handle.net/10468/5017
dc.identifier.volume42
dc.language.isoenen
dc.publisherOxford University Pressen
dc.relation.urihttps://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gku386
dc.rights© 2014, the Authors. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.en
dc.rights.urihttps://creativecommons.org/licenses/by/3.0/
dc.subjectSite transfer RNAen
dc.subjectMessenger RNAen
dc.subjectGene expressionen
dc.subjectTranslational controlen
dc.subjectProkaryotic genomesen
dc.subjectMutational analysisen
dc.subjectBacterial genesen
dc.subjectCoding regionsen
dc.subjectP siteen
dc.subjectSequenceen
dc.titleAnalysis of tetra- and hepta-nucleotides motifs promoting -1 ribosomal frameshifting in Escherichia colien
dc.typeArticle (peer-reviewed)en
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