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

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dc.contributor.author Sharma, Virag
dc.contributor.author Prère, Marie-Francoise
dc.contributor.author Canal, Isabelle
dc.contributor.author Firth, Andrew E.
dc.contributor.author Atkins, John F.
dc.contributor.author Baranov, Pavel V.
dc.contributor.author Fayet, Olivier
dc.date.accessioned 2017-11-14T13:24:30Z
dc.date.available 2017-11-14T13:24:30Z
dc.date.issued 2014
dc.identifier.citation 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 en
dc.identifier.volume 42
dc.identifier.issued 11
dc.identifier.startpage 7210
dc.identifier.endpage 7225
dc.identifier.issn 0305-1048
dc.identifier.issn 1362-4962
dc.identifier.uri http://hdl.handle.net/10468/5017
dc.identifier.doi 10.1093/nar/gku386
dc.description.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. en
dc.description.sponsorship Centre 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.format.mimetype application/pdf en
dc.language.iso en en
dc.publisher Oxford University Press en
dc.relation.uri https://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.uri https://creativecommons.org/licenses/by/3.0/
dc.subject Site transfer RNA en
dc.subject Messenger RNA en
dc.subject Gene expression en
dc.subject Translational control en
dc.subject Prokaryotic genomes en
dc.subject Mutational analysis en
dc.subject Bacterial genes en
dc.subject Coding regions en
dc.subject P site en
dc.subject Sequence en
dc.title Analysis of tetra- and hepta-nucleotides motifs promoting -1 ribosomal frameshifting in Escherichia coli en
dc.type Article (peer-reviewed) en
dc.internal.authorcontactother John F. Atkins, Biochemistry, University College Cork , Cork, Ireland T: +353-21-490-3000. E: j.atkins@ucc.ie en
dc.internal.availability Full text available en
dc.description.version Published Version en
dc.internal.rssid 258499763
dc.contributor.funder Science Foundation Ireland
dc.contributor.funder Wellcome Trust
dc.contributor.funder Agence Nationale de la Recherche
dc.contributor.funder Université Toulouse III - Paul Sabatier
dc.contributor.funder Centre National de la Recherche Scientifique
dc.description.status Peer reviewed en
dc.identifier.journaltitle Nucleic Acids Research en
dc.internal.IRISemailaddress j.atkins@ucc.ie en


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© 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. Except where otherwise noted, this item's license is described as © 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.
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