Identification of the nature of reading frame transitions observed in prokaryotic genomes

Show simple item record

dc.contributor.author Antonov, Ivan
dc.contributor.author Coakley, Arthur
dc.contributor.author Atkins, John F.
dc.contributor.author Baranov, Pavel V.
dc.contributor.author Borodovsky, Mark
dc.date.accessioned 2017-11-14T13:24:30Z
dc.date.available 2017-11-14T13:24:30Z
dc.date.issued 2013
dc.identifier.citation Antonov, I., Coakley, A., Atkins, J. F., Baranov, P. V. and Borodovsky, M. (2013) 'Identification of the nature of reading frame transitions observed in prokaryotic genomes', Nucleic Acids Research, 41(13), pp. 6514-6530. doi: 10.1093/nar/gkt274 en
dc.identifier.volume 41
dc.identifier.issued 13
dc.identifier.startpage 6514
dc.identifier.endpage 6530
dc.identifier.issn 0305-1048
dc.identifier.uri http://hdl.handle.net/10468/5019
dc.identifier.doi 10.1093/nar/gkt274
dc.description.abstract Our goal was to identify evolutionary conserved frame transitions in protein coding regions and to uncover an underlying functional role of these structural aberrations. We used the ab initio frameshift prediction program, GeneTack, to detect reading frame transitions in 206 991 genes (fs-genes) from 1106 complete prokaryotic genomes. We grouped 102 731 fs-genes into 19 430 clusters based on sequence similarity between protein products (fs-proteins) as well as conservation of predicted position of the frameshift and its direction. We identified 4010 pseudogene clusters and 146 clusters of fs-genes apparently using recoding (local deviation from using standard genetic code) due to possessing specific sequence motifs near frameshift positions. Particularly interesting was finding of a novel type of organization of the dnaX gene, where recoding is required for synthesis of the longer subunit, tau. We selected 20 clusters of predicted recoding candidates and designed a series of genetic constructs with a reporter gene or affinity tag whose expression would require a frameshift event. Expression of the constructs in Escherichia coli demonstrated enrichment of the set of candidates with sequences that trigger genuine programmed ribosomal frameshifting; we have experimentally confirmed four new families of programmed frameshifts. en
dc.description.sponsorship USA National Institute of Health (HG000783); Wellcome Trust (094423) 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/gkt274
dc.rights © 2013, the Authors. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), 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 Polymerase III holoenzyme en
dc.subject Simple sequence repeats en
dc.subject Escherichia-coli en
dc.subject Messenger RNA en
dc.subject Transcriptional slippage en
dc.subject Gene expression en
dc.subject Phase variation en
dc.subject Release factor en
dc.subject Gamma subunit en
dc.subject P site en
dc.title Identification of the nature of reading frame transitions observed in prokaryotic genomes en
dc.type Article (peer-reviewed) en
dc.internal.authorcontactother Pavel V. Baranov, 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.description.version Published Version en
dc.internal.rssid 243942257
dc.contributor.funder Science Foundation Ireland
dc.contributor.funder Wellcome Trust
dc.contributor.funder National Institutes of Health
dc.description.status Peer reviewed en
dc.identifier.journaltitle Nucleic Acids Research en
dc.internal.IRISemailaddress p.baranov@ucc.ie en
dc.internal.IRISemailaddress j.atkins@ucc.ie en
dc.relation.project info:eu-repo/grantAgreement/SFI/SFI Principal Investigator Programme (PI)/08/IN.1/B1889/IE/Altered Genetic Code Readout/


Files in this item

This item appears in the following Collection(s)

Show simple item record

© 2013, the Authors. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), 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 © 2013, the Authors. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
This website uses cookies. By using this website, you consent to the use of cookies in accordance with the UCC Privacy and Cookies Statement. For more information about cookies and how you can disable them, visit our Privacy and Cookies statement