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

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dc.contributor.authorAntonov, Ivan
dc.contributor.authorCoakley, Arthur
dc.contributor.authorAtkins, John F.
dc.contributor.authorBaranov, Pavel V.
dc.contributor.authorBorodovsky, Mark
dc.contributor.funderScience Foundation Ireland
dc.contributor.funderWellcome Trust
dc.contributor.funderNational Institutes of Health
dc.date.accessioned2017-11-14T13:24:30Z
dc.date.available2017-11-14T13:24:30Z
dc.date.issued2013
dc.description.abstractOur 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.sponsorshipUSA National Institute of Health (HG000783); Wellcome Trust (094423)en
dc.description.statusPeer revieweden
dc.description.versionPublished Versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.citationAntonov, 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/gkt274en
dc.identifier.doi10.1093/nar/gkt274
dc.identifier.endpage6530
dc.identifier.issn0305-1048
dc.identifier.issued13
dc.identifier.journaltitleNucleic Acids Researchen
dc.identifier.startpage6514
dc.identifier.urihttps://hdl.handle.net/10468/5019
dc.identifier.volume41
dc.language.isoenen
dc.publisherOxford University Pressen
dc.relation.projectinfo:eu-repo/grantAgreement/SFI/SFI Principal Investigator Programme (PI)/08/IN.1/B1889/IE/Altered Genetic Code Readout/
dc.relation.urihttps://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.urihttps://creativecommons.org/licenses/by/3.0/
dc.subjectPolymerase III holoenzymeen
dc.subjectSimple sequence repeatsen
dc.subjectEscherichia-colien
dc.subjectMessenger RNAen
dc.subjectTranscriptional slippageen
dc.subjectGene expressionen
dc.subjectPhase variationen
dc.subjectRelease factoren
dc.subjectGamma subuniten
dc.subjectP siteen
dc.titleIdentification of the nature of reading frame transitions observed in prokaryotic genomesen
dc.typeArticle (peer-reviewed)en
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