dc.contributor.author |
Sharma, Virag |
|
dc.contributor.author |
Prère, Marie-Francoise |
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dc.contributor.author |
Canal, Isabelle |
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dc.contributor.author |
Firth, Andrew E. |
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dc.contributor.author |
Atkins, John F. |
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dc.contributor.author |
Baranov, Pavel V. |
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dc.contributor.author |
Fayet, Olivier |
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dc.date.accessioned |
2017-11-14T13:24:30Z |
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dc.date.available |
2017-11-14T13:24:30Z |
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dc.date.issued |
2014 |
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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 |
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dc.identifier.issued |
11 |
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dc.identifier.startpage |
7210 |
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dc.identifier.endpage |
7225 |
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dc.identifier.issn |
0305-1048 |
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dc.identifier.issn |
1362-4962 |
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dc.identifier.uri |
http://hdl.handle.net/10468/5017 |
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dc.identifier.doi |
10.1093/nar/gku386 |
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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 |
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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/ |
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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 |
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dc.type |
Article (peer-reviewed) |
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dc.internal.authorcontactother |
John F. Atkins, Biochemistry, University College Cork , Cork, Ireland T: +353-21-490-3000. E: j.atkins@ucc.ie |
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dc.internal.availability |
Full text available |
en |
dc.description.version |
Published Version |
en |
dc.internal.rssid |
258499763 |
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dc.contributor.funder |
Science Foundation Ireland
|
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dc.contributor.funder |
Wellcome Trust
|
|
dc.contributor.funder |
Agence Nationale de la Recherche
|
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dc.contributor.funder |
Université Toulouse III - Paul Sabatier
|
|
dc.contributor.funder |
Centre National de la Recherche Scientifique
|
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dc.description.status |
Peer reviewed |
en |
dc.identifier.journaltitle |
Nucleic Acids Research |
en |
dc.internal.IRISemailaddress |
j.atkins@ucc.ie |
en |