{"id":{"repo_id":"cambridge","oai_identifier":"oai:www.repository.cam.ac.uk:1810/374271"},"canonical_url":"https://search.dev.ndltd.org/etd/cambridge/oai:www.repository.cam.ac.uk:1810/374271","repository":{"repo_id":"cambridge","name":"Cambridge University","base_url":"https://api.repository.cam.ac.uk/server/oai/request"},"display":{"title":"RNA regulatory elements and translational control","abstract":"Regulation of RNA translation is crucial for optimal allocation of resources and co-ordinated production of cellular machinery, which allows maintenance of physiological functions, response to environmental stimuli, and control of virulence to establish an infection. In this work, the translational landscape of *Salmonella* Typhimurium and *Listeria monocytogenes* was analysed using a ribosome profiling method adapted for examination of bacteria which yielded single-nucleotide-resolution data. The ribosome profiles in combination with parallel RNA-Seq data were used to examine genetic elements that control translation, and were found to differ between *Salmonella* and *Listeria*. In *Listeria*, we have found that a subset of efficiently translated genes had ribosomal footprints seven nucleotides upstream of the initiation position, which indicates the existence of a novel translation initiation mechanism. Moreover, the high resolution of the data allowed us to identify novel open reading frames. The bacterial ribosome profiling method was then used to examine cultured *Salmonella* as it transitions from the exponential phase towards the stationary phase, and investigated the response of *Salmonella* at four time points after application of acid stress. The project characterized changes in the expression of genes encoding complexes involved in virulence, and response to low pH. Furthermore, a ribosome profile of the *Cowpea mosaic virus*, a model plant RNA virus, was obtained during an infection of *Nicotiana benthamiana*. The results show that ribosomes pause at four sites during viral polyprotein synthesis. They have confirmed the existence of a putative upstream open reading frame and indicated the possible existence of two additional uORFs. And finally, the work focussed on a plant RNA ThermoSwitch. I established a reporter-based experiment used to test the effect of ThermoSwitch sequences in a transient expression system in *N. benthamiana*. The results mark a step towards the development of a plant thermosensitive regulatory system with potential application in molecular farming. The project has described a number of translational features and genetic elements involved in translational regulation, contributing towards our understanding of the physiology and virulence of the examined pathogens, and provides basis for experiments characterizing these features further.","abstract_html":"Regulation of RNA translation is crucial for optimal allocation of resources and co-ordinated production of cellular machinery, which allows maintenance of physiological functions, response to environmental stimuli, and control of virulence to establish an infection. In this work, the translational landscape of *Salmonella* Typhimurium and *Listeria monocytogenes* was analysed using a ribosome profiling method adapted for examination of bacteria which yielded single-nucleotide-resolution data. The ribosome profiles in combination with parallel RNA-Seq data were used to examine genetic elements that control translation, and were found to differ between *Salmonella* and *Listeria*. In *Listeria*, we have found that a subset of efficiently translated genes had ribosomal footprints seven nucleotides upstream of the initiation position, which indicates the existence of a novel translation initiation mechanism. Moreover, the high resolution of the data allowed us to identify novel open reading frames. The bacterial ribosome profiling method was then used to examine cultured *Salmonella* as it transitions from the exponential phase towards the stationary phase, and investigated the response of *Salmonella* at four time points after application of acid stress. The project characterized changes in the expression of genes encoding complexes involved in virulence, and response to low pH. Furthermore, a ribosome profile of the *Cowpea mosaic virus*, a model plant RNA virus, was obtained during an infection of *Nicotiana benthamiana*. The results show that ribosomes pause at four sites during viral polyprotein synthesis. They have confirmed the existence of a putative upstream open reading frame and indicated the possible existence of two additional uORFs. And finally, the work focussed on a plant RNA ThermoSwitch. I established a reporter-based experiment used to test the effect of ThermoSwitch sequences in a transient expression system in *N. benthamiana*. The results mark a step towards the development of a plant thermosensitive regulatory system with potential application in molecular farming. The project has described a number of translational features and genetic elements involved in translational regulation, contributing towards our understanding of the physiology and virulence of the examined pathogens, and provides basis for experiments characterizing these features further.","abstract_has_math":false,"creators":["Lastovka, Filip"],"institution":"University of Cambridge","degree_name":"Doctor of Philosophy (PhD)","degree_level":"Doctoral","degree_discipline":null,"degree_department":null,"school":null,"contributors":[],"advisors":["Chung, Betty"],"committee_chairs":[],"committee_members":[],"year":2023,"date_issued":"2023-12-30","date_published":"2023-12-30","updated_at":"2026-07-22T22:24:31Z","subjects":["ribosome profiling","RNA","translation"],"languages":["eng"],"rights":[],"rights_urls":["https://apollo8-f-pro.lib.cam.ac.uk/bitstreams/96a72184-1638-4cc2-8136-dd5be5c60f1d/download","https://www.rioxx.net/licenses/all-rights-reserved/"],"identifier_entries":[]},"links":{"outbound_url":"https://doi.org/10.17863/CAM.112390","outbound_label":"DOI","outbound_source":"dc:identifier.doi"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor.advisor","label":"Advisor","values":["Chung, Betty"]},{"key":"dc:creator","label":"Author","values":["Lastovka, Filip"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.issued","label":"Date","values":["2023-12-30"]},{"key":"dc:publisher.institution","label":"Dc Publisher Institution","values":["University of Cambridge"]},{"key":"dc:relation.isreferencedby.uri","label":"Dc Relation Isreferencedby URI","values":["https://www.repository.cam.ac.uk/handle/1810/374271"]},{"key":"dc:type","label":"Dc Type","values":["Thesis"]},{"key":"dc:type.qualificationlevel","label":"Dc Type Qualificationlevel","values":["Doctoral"]},{"key":"dc:type.qualificationname","label":"Dc Type Qualificationname","values":["Doctor of Philosophy (PhD)"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["ribosome profiling","RNA","translation"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["eng"]},{"key":"dc:rights","label":"Dc Rights","values":["https://apollo8-f-pro.lib.cam.ac.uk/bitstreams/96a72184-1638-4cc2-8136-dd5be5c60f1d/download","https://www.rioxx.net/licenses/all-rights-reserved/"]},{"key":"dc:rights.embargodate","label":"Dc Rights Embargodate","values":["2028-10-01"]},{"key":"dc:rights.embargotype","label":"Dc Rights Embargotype","values":["embargo"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier.doi","label":"DOI","values":["https://doi.org/10.17863/CAM.112390"]},{"key":"dc:identifier.uri","label":"Identifier URI","values":["https://apollo8-f-pro.lib.cam.ac.uk/bitstreams/bcc5a6d3-1c2d-406e-a805-b3068bec437b/download"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["Regulation of RNA translation is crucial for optimal allocation of resources and co-ordinated production of cellular machinery, which allows maintenance of physiological functions, response to environmental stimuli, and control of virulence to establish an infection. 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The bacterial ribosome profiling method was then used to examine cultured *Salmonella* as it transitions from the exponential phase towards the stationary phase, and investigated the response of *Salmonella* at four time points after application of acid stress. The project characterized changes in the expression of genes encoding complexes involved in virulence, and response to low pH. Furthermore, a ribosome profile of the *Cowpea mosaic virus*, a model plant RNA virus, was obtained during an infection of *Nicotiana benthamiana*. The results show that ribosomes pause at four sites during viral polyprotein synthesis. They have confirmed the existence of a putative upstream open reading frame and indicated the possible existence of two additional uORFs. And finally, the work focussed on a plant RNA ThermoSwitch. I established a reporter-based experiment used to test the effect of ThermoSwitch sequences in a transient expression system in *N. benthamiana*. 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