Structural basis of ribosomal frameshifting

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dc.availability.bitstreamcontrolled
dc.check.date2025-09-30
dc.contributor.advisorAtkins, John F.en
dc.contributor.authorBhatt, Pramod R.
dc.contributor.funderIrish Research Councilen
dc.date.accessioned2022-05-23T14:29:55Z
dc.date.available2022-05-23T14:29:55Z
dc.date.issued2021-10-10
dc.date.submitted2021-10-10
dc.description.abstractVersatility in genetic decoding enriches gene expression. Programmed shifting of the reading frame during translation is a prominent feature productively utilized in probably all life forms. While the occurrences, function, and mechanistic components have been identified for many instances of frameshifting, structural understanding of their basis at the atomic level has been limited to the individual components in isolation. Here, I present atomic level information of the decoding apparatus relevant to both -1 and +1 frameshifting. The +1 frameshifting event investigated is that of a sensor and effector of an autoregulatory circuit present in the common ancestor between yeast and humans. In regulating intracellular polyamine levels, the mammalian antizyme 2 frameshifting studied interacts with ornithine decarboxylase and c-myc. The polyamine spermidine is shown here to be present proximal to but not interfering with the peptidyl transferase center, making stabilizing interactions with the terminal phosphate of the P-site tRNA. Spermidine occupancy at this location is inferred to preclude binding of the translation factor eIF5A by occlusion of its hypusine moiety. Visualization of the nascent chain reveals a network of interactions with key residues of the peptide exit tunnel that gate the transit of the growing polypeptide. The -1 frameshifting event investigated is that required by SARS-CoV-2, the causative virus of the COVID-19 pandemic. The downstream RNA element that stimulates frameshifting is seen to adopt a corkscrew-shaped 3-stemmed pseudoknot structure that lodges itself at the entrance of the ribosomal mRNA channel. Distinct functional interactions of the nascent chain with the ribosome exit tunnel are observed while the distal end of the nascent peptide begins to undergo co-translational folding into a zinc finger motif. The study highlights the frameshift-inhibitory properties of Merafloxacin, a small molecule that inhibits propagation of SARS-CoV-2.en
dc.description.statusNot peer revieweden
dc.description.versionAccepted Versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.citationBhatt, P. R. 2021. Structural basis of ribosomal frameshifting. PhD Thesis, University College Cork.en
dc.identifier.endpage177en
dc.identifier.urihttps://hdl.handle.net/10468/13217
dc.language.isoenen
dc.publisherUniversity College Corken
dc.relation.projectIrish Research Council (4100 - R18814)en
dc.rights© 2021, Pramod Raghupathi Bhatt.en
dc.rights.urihttps://creativecommons.org/licenses/by-nc-nd/4.0/en
dc.subjectRibosomal frameshiftingen
dc.subjectCryo-electron microscopyen
dc.subjectTranslationen
dc.subjectSARS-CoV-2en
dc.titleStructural basis of ribosomal frameshiftingen
dc.typeDoctoral thesisen
dc.type.qualificationlevelDoctoralen
dc.type.qualificationnamePhD - Doctor of Philosophyen
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