{"id":{"repo_id":"uic","oai_identifier":"oai:figshare.com:article/31451293"},"canonical_url":"https://search.dev.ndltd.org/etd/uic/oai:figshare.com:article/31451293","repository":{"repo_id":"uic","name":"University of Illinois - Chicago","base_url":"https://api.figshare.com/v2/oai"},"display":{"title":"The Impact of Depleting the Essential Bacterial Enzyme Peptidyl-tRNA Hydrolase on Translation","abstract":"Peptidyl-tRNA hydrolase (Pth) is an essential bacterial enzyme that recycles peptidyl-tRNAs (pep-tRNAs) by hydrolyzing the ester bond between the tRNA and the peptide. The best-characterized function of Pth is salvaging free pep-tRNAs that dissociate from the ribosome during translation to prevent starvation for translation-usable tRNAs. Depletion of Pth leads to the accumulation of pep-tRNAs, rapid inhibition of translation, and cell death. Recent studies have demonstrated that Pth can process pep-tRNAs associated with large ribosomal subunits and possibly even translating ribosomes. The discovery of these additional Pth substrates demonstrates that the physiological role of Pth may be more complex than was previously thought and brings longstanding beliefs about the essentiality of Pth into question. We used genome-wide techniques to characterize the effects of the loss of Pth on translation and searched for factors that can compensate for its depletion in Escherichia coli to expand our understanding of the physiological role of Pth. In a thermosensitive Pth mutant, pth(Ts), we found that Pth depletion promotes ribosome stalling at many codons, especially at the early codons of ORFs. This broad stalling leads us to conclude that the cell may starve for many tRNAs rather than just tRNALys, as was previously envisioned. We discovered that the overexpression of a protein of unknown function, YajQ, partially restores the growth of cells depleted of Pth. YajQ overexpression globally reduces the ribosome stalling caused by Pth depletion at most codons, suggesting a possible role for YajQ in translation. To disentangle the effects of heat shock in investigating the functions of Pth, we created a heat shock-independent model of Pth depletion, in which Pth can be depleted at the temperature optimal for cell growth. Using this model, we found that Pth depletion still leads to widespread ribosome stalling, though it occurred at a few specific codons. Intriguingly, we found that overexpression of tRNAs that recognize the codons at which stalling occurred does not improve survival of cells during Pth depletion, suggesting that additional functions of Pth beyond recycling free pep-tRNAs may play a key role in the essentiality of this enzyme.","abstract_html":"Peptidyl-tRNA hydrolase (Pth) is an essential bacterial enzyme that recycles peptidyl-tRNAs (pep-tRNAs) by hydrolyzing the ester bond between the tRNA and the peptide. The best-characterized function of Pth is salvaging free pep-tRNAs that dissociate from the ribosome during translation to prevent starvation for translation-usable tRNAs. Depletion of Pth leads to the accumulation of pep-tRNAs, rapid inhibition of translation, and cell death. Recent studies have demonstrated that Pth can process pep-tRNAs associated with large ribosomal subunits and possibly even translating ribosomes. The discovery of these additional Pth substrates demonstrates that the physiological role of Pth may be more complex than was previously thought and brings longstanding beliefs about the essentiality of Pth into question. We used genome-wide techniques to characterize the effects of the loss of Pth on translation and searched for factors that can compensate for its depletion in Escherichia coli to expand our understanding of the physiological role of Pth. In a thermosensitive Pth mutant, pth(Ts), we found that Pth depletion promotes ribosome stalling at many codons, especially at the early codons of ORFs. This broad stalling leads us to conclude that the cell may starve for many tRNAs rather than just tRNALys, as was previously envisioned. We discovered that the overexpression of a protein of unknown function, YajQ, partially restores the growth of cells depleted of Pth. YajQ overexpression globally reduces the ribosome stalling caused by Pth depletion at most codons, suggesting a possible role for YajQ in translation. To disentangle the effects of heat shock in investigating the functions of Pth, we created a heat shock-independent model of Pth depletion, in which Pth can be depleted at the temperature optimal for cell growth. Using this model, we found that Pth depletion still leads to widespread ribosome stalling, though it occurred at a few specific codons. Intriguingly, we found that overexpression of tRNAs that recognize the codons at which stalling occurred does not improve survival of cells during Pth depletion, suggesting that additional functions of Pth beyond recycling free pep-tRNAs may play a key role in the essentiality of this enzyme.","abstract_has_math":false,"creators":["Alexander Kenyon Richardson (23291515)"],"institution":null,"degree_name":null,"degree_level":null,"degree_discipline":null,"degree_department":null,"school":null,"contributors":[],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2025,"date_issued":"2025-12-01T00:00:00Z","date_published":"2025-12-01T00:00:00Z","updated_at":"2026-07-27T21:34:24Z","subjects":["Biology, Molecular","Chemistry, Biochemistry","Biology, Microbiology"],"languages":[],"rights":["In Copyright"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://doi.org/10.25417/uic.31451293.v1","outbound_label":"DOI","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:creator","label":"Author","values":["Alexander Kenyon Richardson (23291515)"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2025-12-01T00:00:00Z"]},{"key":"dc:relation","label":"Dc Relation","values":["https://figshare.com/articles/thesis/The_Impact_of_Depleting_the_Essential_Bacterial_Enzyme_Peptidyl-tRNA_Hydrolase_on_Translation/31451293"]},{"key":"dc:type","label":"Dc Type","values":["Text","Thesis"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Biology, Molecular","Chemistry, Biochemistry","Biology, Microbiology"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:rights","label":"Dc Rights","values":["In Copyright"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["10.25417/uic.31451293.v1"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Peptidyl-tRNA hydrolase (Pth) is an essential bacterial enzyme that recycles peptidyl-tRNAs (pep-tRNAs) by hydrolyzing the ester bond between the tRNA and the peptide. The best-characterized function of Pth is salvaging free pep-tRNAs that dissociate from the ribosome during translation to prevent starvation for translation-usable tRNAs. Depletion of Pth leads to the accumulation of pep-tRNAs, rapid inhibition of translation, and cell death. Recent studies have demonstrated that Pth can process pep-tRNAs associated with large ribosomal subunits and possibly even translating ribosomes. The discovery of these additional Pth substrates demonstrates that the physiological role of Pth may be more complex than was previously thought and brings longstanding beliefs about the essentiality of Pth into question. We used genome-wide techniques to characterize the effects of the loss of Pth on translation and searched for factors that can compensate for its depletion in Escherichia coli to expand our understanding of the physiological role of Pth. In a thermosensitive Pth mutant, pth(Ts), we found that Pth depletion promotes ribosome stalling at many codons, especially at the early codons of ORFs. This broad stalling leads us to conclude that the cell may starve for many tRNAs rather than just tRNALys, as was previously envisioned. We discovered that the overexpression of a protein of unknown function, YajQ, partially restores the growth of cells depleted of Pth. YajQ overexpression globally reduces the ribosome stalling caused by Pth depletion at most codons, suggesting a possible role for YajQ in translation. To disentangle the effects of heat shock in investigating the functions of Pth, we created a heat shock-independent model of Pth depletion, in which Pth can be depleted at the temperature optimal for cell growth. Using this model, we found that Pth depletion still leads to widespread ribosome stalling, though it occurred at a few specific codons. Intriguingly, we found that overexpression of tRNAs that recognize the codons at which stalling occurred does not improve survival of cells during Pth depletion, suggesting that additional functions of Pth beyond recycling free pep-tRNAs may play a key role in the essentiality of this enzyme."]},{"key":"dc:title","label":"Title","values":["The Impact of Depleting the Essential Bacterial Enzyme Peptidyl-tRNA Hydrolase on Translation"]}]}],"canonical_facts":{"dc:creator":["Alexander Kenyon Richardson (23291515)"],"dc:date":["2025-12-01T00:00:00Z"],"dc:description":["Peptidyl-tRNA hydrolase (Pth) is an essential bacterial enzyme that recycles peptidyl-tRNAs (pep-tRNAs) by hydrolyzing the ester bond between the tRNA and the peptide. The best-characterized function of Pth is salvaging free pep-tRNAs that dissociate from the ribosome during translation to prevent starvation for translation-usable tRNAs. Depletion of Pth leads to the accumulation of pep-tRNAs, rapid inhibition of translation, and cell death. Recent studies have demonstrated that Pth can process pep-tRNAs associated with large ribosomal subunits and possibly even translating ribosomes. The discovery of these additional Pth substrates demonstrates that the physiological role of Pth may be more complex than was previously thought and brings longstanding beliefs about the essentiality of Pth into question. We used genome-wide techniques to characterize the effects of the loss of Pth on translation and searched for factors that can compensate for its depletion in Escherichia coli to expand our understanding of the physiological role of Pth. In a thermosensitive Pth mutant, pth(Ts), we found that Pth depletion promotes ribosome stalling at many codons, especially at the early codons of ORFs. This broad stalling leads us to conclude that the cell may starve for many tRNAs rather than just tRNALys, as was previously envisioned. We discovered that the overexpression of a protein of unknown function, YajQ, partially restores the growth of cells depleted of Pth. YajQ overexpression globally reduces the ribosome stalling caused by Pth depletion at most codons, suggesting a possible role for YajQ in translation. To disentangle the effects of heat shock in investigating the functions of Pth, we created a heat shock-independent model of Pth depletion, in which Pth can be depleted at the temperature optimal for cell growth. Using this model, we found that Pth depletion still leads to widespread ribosome stalling, though it occurred at a few specific codons. Intriguingly, we found that overexpression of tRNAs that recognize the codons at which stalling occurred does not improve survival of cells during Pth depletion, suggesting that additional functions of Pth beyond recycling free pep-tRNAs may play a key role in the essentiality of this enzyme."],"dc:identifier":["10.25417/uic.31451293.v1"],"dc:relation":["https://figshare.com/articles/thesis/The_Impact_of_Depleting_the_Essential_Bacterial_Enzyme_Peptidyl-tRNA_Hydrolase_on_Translation/31451293"],"dc:rights":["In Copyright"],"dc:subject":["Biology, Molecular","Chemistry, Biochemistry","Biology, Microbiology"],"dc:title":["The Impact of Depleting the Essential Bacterial Enzyme Peptidyl-tRNA Hydrolase on Translation"],"dc:type":["Text","Thesis"]},"updated_at":"2026-07-27T21:34:24Z"}