Recoding and reassignment in protists

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dc.contributor.advisor Baranov, Pavel V. en
dc.contributor.author Heaphy, Stephen M.
dc.date.accessioned 2018-05-16T11:11:42Z
dc.date.issued 2018
dc.date.submitted 2018
dc.identifier.citation Heaphy, S. 2018. Recoding and reassignment in protists. PhD Thesis, University College Cork. en
dc.identifier.endpage 112 en
dc.identifier.uri http://hdl.handle.net/10468/6122
dc.description.abstract During mRNA translation the ribosome reads each codon (nucleotide triplet) with a specific meaning. The standard genetic code comprises 61 sense-codons for specifying the 20 standard amino acids during elongation and three anti-sense codons which signal termination. While variations to the standard rules of genetic decoding are widely acknowledged, recent advances in next generation sequencing techniques have provided a wealth of new examples across many species. In this thesis, I provide evidence of novel decoding mechanisms in protists, as identified through bioinformatics analysis. To begin with I analysed the genomes of two ciliate species, Euplotes crassus and E. focardii. In combination with the analysis of E. crassus transcriptome using ribosome profiling, I determined over 1,700 cases of ribosomal frameshifting (22% of genes analysed) in E. crassus. I identified 47 codons upstream of a stop signal which directs the ribosome to either the +1 or +2 reading frames. Termination only occurs in the context of the poly-A tail. In addition I analysed the transcriptomes of over 200 diverse protist species for the protein ornithine decarboxylase antizyme, a key negative regulator of cellular polyamine synthesis. The synthesis of this protein usually requires a +1 ribosomal frameshift at the end of the first open reading frame. In this study I identified a novel mechanism of stop codon readthrough to regulate antizyme production in dinoflagellates and single ORF sequences from other protist phyla. Further I analysed transcriptomes of diverse ciliate organisms to characterize stop codon reassignments in their genetic codes. In addition to finding novel stop codon reassignments, I identified an organism, Condylostoma magnum where all three stop codons TAA, TAG & TGA have been reassigned to sense codons. All three stop codons are enriched at the expected positions of translation termination sites which occur at a short distance from the 3’ poly-A tail. en
dc.format.mimetype application/pdf en
dc.language.iso en en
dc.publisher University College Cork en
dc.rights © 2018, Stephen Heaphy. en
dc.rights.uri http://creativecommons.org/licenses/by-nc-nd/3.0/ en
dc.subject Bioinformatics en
dc.title Recoding and reassignment in protists en
dc.type Doctoral thesis en
dc.type.qualificationlevel Doctoral en
dc.type.qualificationname PhD en
dc.internal.availability Full text available en
dc.description.version Accepted Version
dc.contributor.funder Science Foundation Ireland en
dc.description.status Not peer reviewed en
dc.internal.school Biochemistry and Cell Biology en
dc.check.reason This thesis contains data which has not yet been published en
dc.check.opt-out Not applicable en
dc.thesis.opt-out false
dc.check.embargoformat Apply the embargo to the e-thesis on CORA (If you have submitted an e-thesis and want to embargo it on CORA) en
ucc.workflow.supervisor p.baranov@ucc.ie
dc.internal.conferring Summer 2018 en


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