Recoding and reassignment in protists
| 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 |
| dc.check.opt-out | Not applicable | en |
| dc.check.reason | This thesis contains data which has not yet been published | en |
| dc.contributor.advisor | Baranov, Pavel V. | en |
| dc.contributor.author | Heaphy, Stephen M. | |
| dc.contributor.funder | Science Foundation Ireland | en |
| dc.date.accessioned | 2018-05-16T11:11:42Z | |
| dc.date.issued | 2018 | |
| dc.date.submitted | 2018 | |
| 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.description.status | Not peer reviewed | en |
| dc.description.version | Accepted Version | |
| dc.format.mimetype | application/pdf | en |
| 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 | https://hdl.handle.net/10468/6122 | |
| 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.thesis.opt-out | false | |
| dc.title | Recoding and reassignment in protists | en |
| dc.type | Doctoral thesis | en |
| dc.type.qualificationlevel | Doctoral | en |
| dc.type.qualificationname | PhD | en |
| ucc.workflow.supervisor | p.baranov@ucc.ie |
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