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oai:cora.ucc.ie:10468/61222023-04-04T07:08:44Zcom_10468_67com_10468_5com_10468_388com_10468_1col_10468_805col_10468_389col_10468_140

Apply the embargo to the e-thesis on CORA (If you have submitted an e-thesis and want to embargo it on CORA) Not applicable This thesis contains data which has not yet been published Baranov, Pavel V. Heaphy, Stephen M. Science Foundation Ireland 2018-05-16T11:11:42Z 2018 2018 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. Not peer reviewed Accepted Version application/pdf Heaphy, S. 2018. Recoding and reassignment in protists. PhD Thesis, University College Cork. 112 https://hdl.handle.net/10468/6122 en University College Cork © 2018, Stephen Heaphy. http://creativecommons.org/licenses/by-nc-nd/3.0/ Bioinformatics false Recoding and reassignment in protists Doctoral thesis Doctoral PhD p.baranov@ucc.ieinfo:eu-repo/semantics/openAccess