Novel ciliate genetic code variants including the reassignment of all three stop codons to sense codons in Condylostoma magnum

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dc.contributor.author Heaphy, Stephen M.
dc.contributor.author Mariotti, Marco
dc.contributor.author Gladyshev, Vadim N.
dc.contributor.author Atkins, John F.
dc.contributor.author Baranov, Pavel V.
dc.date.accessioned 2016-11-22T15:08:20Z
dc.date.available 2016-11-22T15:08:20Z
dc.date.issued 2016-08-08
dc.identifier.citation Heaphy, Stephen M.; Mariotti, Marco; Gladyshev, Vadim N.; Atkins, John F.; Baranov, Pavel V. (2016) 'Novel ciliate genetic code variants including the reassignment of all three stop codons to sense codons in Condylostoma magnum'. Molecular Biology And Evolution, 33 (1111):2885-2889. doi: 10.1093/molbev/msw166 en
dc.identifier.volume 33 en
dc.identifier.issued 1111 en
dc.identifier.startpage 2885 en
dc.identifier.endpage 2889 en
dc.identifier.issn 0737-4038
dc.identifier.uri http://hdl.handle.net/10468/3302
dc.identifier.doi 10.1093/molbev/msw166
dc.description.abstract mRNA translation in many ciliates utilizes variant genetic codes where stop codons are reassigned to specify amino acids. To characterize the repertoire of ciliate genetic codes, we analyzed ciliate transcriptomes from marine environments. Using codon substitution frequencies in ciliate protein-coding genes and their orthologs, we inferred the genetic codes of 24 ciliate species. Nine did not match genetic code tables currently assigned by NCBI. Surprisingly, we identified a novel genetic code where all three standard stop codons (TAA, TAG, and TGA) specify amino acids in Condylostoma magnum. We provide evidence suggesting that the functions of these codons in C. magnum depend on their location within mRNA. They are decoded as amino acids at internal positions, but specify translation termination when in close proximity to an mRNA 3' end. The frequency of stop codons in protein coding sequences of closely related Climacostomum virens suggests that it may represent a transitory state.mRNA translation in many ciliates utilizes variant genetic codes where stop codons are reassigned to specify amino acids. To characterize the repertoire of ciliate genetic codes, we analyzed ciliate transcriptomes from marine environments. Using codon substitution frequencies in ciliate protein-coding genes and their orthologs, we inferred the genetic codes of 24 ciliate species. Nine did not match genetic code tables currently assigned by NCBI. Surprisingly, we identified a novel genetic code where all three standard stop codons (TAA, TAG, and TGA) specify amino acids in Condylostoma magnum. We provide evidence suggesting that the functions of these codons in C. magnum depend on their location within mRNA. They are decoded as amino acids at internal positions, but specify translation termination when in close proximity to an mRNA 3' end. The frequency of stop codons in protein coding sequences of closely related Climacostomum virens suggests that it may represent a transitory state. en
dc.description.sponsorship Science Foundation Ireland (12/IA/1335, 13/1A/1853); National Institute of Health (GM061603) en
dc.format.mimetype application/pdf en
dc.language.iso en en
dc.publisher Oxford University Press en
dc.relation.uri http://mbe.oxfordjournals.org/content/33/11/2885.abstract
dc.rights © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com en
dc.rights.uri http://creativecommons.org/licenses/by-nc/4.0/ en
dc.subject Alternative genetic decoding en
dc.subject Ciliates en
dc.subject Stop codon reassignment en
dc.subject The genetic code en
dc.subject Translation termination en
dc.title Novel ciliate genetic code variants including the reassignment of all three stop codons to sense codons in Condylostoma magnum en
dc.type Article (peer-reviewed) en
dc.internal.authorcontactother Pavel Baranov, School Of Biochemistry & Cell Biology, University College Cork, Cork, Ireland. +353-21-490-3000 Email: p.baranov@ucc.ie en
dc.internal.authorcontactother John F. Atkins, Biochemistry, University College Cork, Cork, Ireland. +353-21-490-3000 Email: j.atkins@ucc.ie en
dc.internal.availability Full text available en
dc.date.updated 2016-11-14T11:49:57Z
dc.description.version Published Version en
dc.internal.rssid 371831538
dc.contributor.funder Science Foundation Ireland en
dc.contributor.funder National Institutes of Health en
dc.description.status Peer reviewed en
dc.identifier.journaltitle Molecular Biology And Evolution en
dc.internal.copyrightchecked No en
dc.internal.licenseacceptance Yes en
dc.internal.IRISemailaddress p.baranov@ucc.ie en
dc.internal.IRISemailaddress 431799807 en


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© The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com Except where otherwise noted, this item's license is described as © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
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