{"id":{"repo_id":"cork","oai_identifier":"oai:cora.ucc.ie:10468/6122"},"canonical_url":"https://search.dev.ndltd.org/etd/cork/oai:cora.ucc.ie:10468/6122","repository":{"repo_id":"cork","name":"University College Cork","base_url":"https://cora.ucc.ie/server/oai/request"},"display":{"title":"Recoding and reassignment in protists","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.","abstract_html":"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.","abstract_has_math":false,"creators":["Heaphy, Stephen M."],"institution":"University College Cork","degree_name":null,"degree_level":null,"degree_discipline":null,"degree_department":null,"school":null,"contributors":[],"advisors":["Baranov, Pavel V."],"committee_chairs":[],"committee_members":[],"year":2018,"date_issued":"2018","date_published":"2018","updated_at":"2026-07-24T01:48:31Z","subjects":["Bioinformatics"],"languages":["en"],"rights":["© 2018, Stephen Heaphy."],"rights_urls":["http://creativecommons.org/licenses/by-nc-nd/3.0/"],"identifier_entries":[]},"links":{"outbound_url":"https://hdl.handle.net/10468/6122","outbound_label":"Handle","outbound_source":"dc:identifier.uri"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor.advisor","label":"Advisor","values":["Baranov, Pavel V."]},{"key":"dc:creator","label":"Author","values":["Heaphy, Stephen M."]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.accessioned","label":"Dc Date Accessioned","values":["2018-05-16T11:11:42Z"]},{"key":"dc:date.issued","label":"Date","values":["2018"]},{"key":"dc:publisher","label":"Institution","values":["University College Cork"]},{"key":"dc:type","label":"Dc Type","values":["Doctoral thesis"]},{"key":"dc:type.qualificationlevel","label":"Dc Type Qualificationlevel","values":["Doctoral"]},{"key":"dc:type.qualificationname","label":"Dc Type Qualificationname","values":["PhD"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Bioinformatics"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language.iso","label":"Language (ISO)","values":["en"]},{"key":"dc:rights","label":"Dc Rights","values":["© 2018, Stephen Heaphy."]},{"key":"dc:rights.uri","label":"Rights URI","values":["http://creativecommons.org/licenses/by-nc-nd/3.0/"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier.uri","label":"Identifier URI","values":["https://hdl.handle.net/10468/6122"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["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."]},{"key":"dc:format.mimetype","label":"Dc Format Mimetype","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["Recoding and reassignment in protists"]}]}],"canonical_facts":{"dc:contributor.advisor":["Baranov, Pavel V."],"dc:creator":["Heaphy, Stephen M."],"dc:date.accessioned":["2018-05-16T11:11:42Z"],"dc:date.issued":["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."],"dc:format.mimetype":["application/pdf"],"dc:identifier.uri":["https://hdl.handle.net/10468/6122"],"dc:language.iso":["en"],"dc:publisher":["University College Cork"],"dc:rights":["© 2018, Stephen Heaphy."],"dc:rights.uri":["http://creativecommons.org/licenses/by-nc-nd/3.0/"],"dc:subject":["Bioinformatics"],"dc:title":["Recoding and reassignment in protists"],"dc:type":["Doctoral thesis"],"dc:type.qualificationlevel":["Doctoral"],"dc:type.qualificationname":["PhD"]},"updated_at":"2026-07-24T01:48:31Z"}