{"id":{"repo_id":"utswmed","oai_identifier":"oai:utswmed-ir.tdl.org:2152.5/10802"},"canonical_url":"https://search.dev.ndltd.org/etd/utswmed/oai:utswmed-ir.tdl.org:2152.5/10802","repository":{"repo_id":"utswmed","name":"University of Texas Southwestern Medical Center","base_url":"https://utswmed-ir.tdl.org/server/oai/request"},"display":{"title":"Investigating Interferon-Inducible Antiviral Effectors Through a Virological and Evolutionary Lens","abstract":"Interferons control viral infection by inducing expression of effector proteins encoded by interferon-stimulated genes (ISGs). The field has focused on identifying antiviral ISG effectors and defining their mechanisms of action. However, fundamental gaps in knowledge about the interferon response remain. For example, it is unknown how many ISGs are required to restrict a particular virus, though it is theorized that numerous ISGs act in concert to achieve viral inhibition. Here, I used CRISPR-based loss-of-function screens to identify a limited set of ISGs that confer interferon-mediated suppression of Venezuelan equine encephalitis virus (VEEV). I show via combinatorial gene targeting that antiviral effectors - ZAP, IFIT3, and IFIT1 - together constitute the majority of interferon-mediated VEEV restriction, while comprising less than 0.5% of the interferon-induced transcriptome. Together, my data suggest a refined model of the antiviral interferon response in which a small subset of "dominant" ISGs may confer the bulk of the inhibition of a given virus. One of these "dominant" ISGs, IFIT1, recognizes and binds to RNAs lacking the 5' features of host mRNAs, resulting in targeted suppression of viral RNA translation. This interaction creates significant host-driven evolutionary pressure, as many viruses have evolved mechanisms to evade IFIT1 antiviral function. However, less is known about the virus-driven pressures that have shaped the antiviral activity of mammalian IFIT1 genes. Here, I used evolutionary approaches to show that the IFIT1 gene is rapidly evolving in multiple mammalian orders, with positive selection acting upon several residues in distinct regions of the protein. In functional assays with IFIT1s spanning diverse mammals, I show that IFIT1 exhibits a range of antiviral phenotypes. Some orthologs lack antiviral activity against viruses that are strongly suppressed by others, such as chimpanzee IFIT1, which does not inhibit VEEV infection. I further determine that IFIT1 from human and one species of bat exhibit potent anti-VEEV activity and strong affinity for VEEV Cap0 RNA, while IFIT1 from chimpanzee does not. Using targeted mutagenesis, I identify residues responsible for chimpanzee IFIT1 loss of anti-VEEV function, some of which are rapidly evolving. Together, my studies provide insight into the influence of evolution on IFIT1 antiviral activity and the antiviral interferon response.","abstract_html":"Interferons control viral infection by inducing expression of effector proteins encoded by interferon-stimulated genes (ISGs). The field has focused on identifying antiviral ISG effectors and defining their mechanisms of action. However, fundamental gaps in knowledge about the interferon response remain. For example, it is unknown how many ISGs are required to restrict a particular virus, though it is theorized that numerous ISGs act in concert to achieve viral inhibition. Here, I used CRISPR-based loss-of-function screens to identify a limited set of ISGs that confer interferon-mediated suppression of Venezuelan equine encephalitis virus (VEEV). I show via combinatorial gene targeting that antiviral effectors - ZAP, IFIT3, and IFIT1 - together constitute the majority of interferon-mediated VEEV restriction, while comprising less than 0.5% of the interferon-induced transcriptome. Together, my data suggest a refined model of the antiviral interferon response in which a small subset of "dominant" ISGs may confer the bulk of the inhibition of a given virus. One of these "dominant" ISGs, IFIT1, recognizes and binds to RNAs lacking the 5' features of host mRNAs, resulting in targeted suppression of viral RNA translation. This interaction creates significant host-driven evolutionary pressure, as many viruses have evolved mechanisms to evade IFIT1 antiviral function. However, less is known about the virus-driven pressures that have shaped the antiviral activity of mammalian IFIT1 genes. Here, I used evolutionary approaches to show that the IFIT1 gene is rapidly evolving in multiple mammalian orders, with positive selection acting upon several residues in distinct regions of the protein. In functional assays with IFIT1s spanning diverse mammals, I show that IFIT1 exhibits a range of antiviral phenotypes. Some orthologs lack antiviral activity against viruses that are strongly suppressed by others, such as chimpanzee IFIT1, which does not inhibit VEEV infection. I further determine that IFIT1 from human and one species of bat exhibit potent anti-VEEV activity and strong affinity for VEEV Cap0 RNA, while IFIT1 from chimpanzee does not. Using targeted mutagenesis, I identify residues responsible for chimpanzee IFIT1 loss of anti-VEEV function, some of which are rapidly evolving. Together, my studies provide insight into the influence of evolution on IFIT1 antiviral activity and the antiviral interferon response.","abstract_has_math":false,"creators":["McDougal, Matthew Bret"],"institution":null,"degree_name":null,"degree_level":null,"degree_discipline":null,"degree_department":null,"school":null,"contributors":["Gammon, Don B.","Pfeiffer, Julie K.","Orchard, Robert C.","Schoggins, John W."],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2026,"date_issued":"2026-06-15T19:42:10Z","date_published":"2026-06-15T19:42:10Z","updated_at":"2026-07-24T05:52:31Z","subjects":["Adaptor Proteins, Signal Transducing","Encephalitis Virus, Venezuelan Equine","Evolution, Molecular","RNA-Binding Proteins","Virus Diseases","Viruses"],"languages":["en"],"rights":[],"rights_urls":[],"identifier_entries":[{"key":"dc:identifier","label":"Identifier","values":["1596185280"],"render_values":[{"text":"1596185280","href":null,"code":true}]}]},"links":{"outbound_url":"https://hdl.handle.net/2152.5/10802","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Gammon, Don B.","Pfeiffer, Julie K.","Orchard, Robert C.","Schoggins, John W."]},{"key":"dc:creator","label":"Author","values":["McDougal, Matthew Bret"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2026-06-15T19:42:10Z","2024-05","May 2024","2026-06-15T19:42:11Z"]},{"key":"dc:type","label":"Dc Type","values":["Thesis","text"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Adaptor Proteins, Signal Transducing","Encephalitis Virus, Venezuelan Equine","Evolution, Molecular","RNA-Binding Proteins","Virus Diseases","Viruses"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://hdl.handle.net/2152.5/10802","1596185280"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Interferons control viral infection by inducing expression of effector proteins encoded by interferon-stimulated genes (ISGs). The field has focused on identifying antiviral ISG effectors and defining their mechanisms of action. However, fundamental gaps in knowledge about the interferon response remain. For example, it is unknown how many ISGs are required to restrict a particular virus, though it is theorized that numerous ISGs act in concert to achieve viral inhibition. Here, I used CRISPR-based loss-of-function screens to identify a limited set of ISGs that confer interferon-mediated suppression of Venezuelan equine encephalitis virus (VEEV). I show via combinatorial gene targeting that antiviral effectors - ZAP, IFIT3, and IFIT1 - together constitute the majority of interferon-mediated VEEV restriction, while comprising less than 0.5% of the interferon-induced transcriptome. Together, my data suggest a refined model of the antiviral interferon response in which a small subset of "dominant" ISGs may confer the bulk of the inhibition of a given virus. One of these "dominant" ISGs, IFIT1, recognizes and binds to RNAs lacking the 5' features of host mRNAs, resulting in targeted suppression of viral RNA translation. This interaction creates significant host-driven evolutionary pressure, as many viruses have evolved mechanisms to evade IFIT1 antiviral function. However, less is known about the virus-driven pressures that have shaped the antiviral activity of mammalian IFIT1 genes. Here, I used evolutionary approaches to show that the IFIT1 gene is rapidly evolving in multiple mammalian orders, with positive selection acting upon several residues in distinct regions of the protein. In functional assays with IFIT1s spanning diverse mammals, I show that IFIT1 exhibits a range of antiviral phenotypes. Some orthologs lack antiviral activity against viruses that are strongly suppressed by others, such as chimpanzee IFIT1, which does not inhibit VEEV infection. I further determine that IFIT1 from human and one species of bat exhibit potent anti-VEEV activity and strong affinity for VEEV Cap0 RNA, while IFIT1 from chimpanzee does not. Using targeted mutagenesis, I identify residues responsible for chimpanzee IFIT1 loss of anti-VEEV function, some of which are rapidly evolving. Together, my studies provide insight into the influence of evolution on IFIT1 antiviral activity and the antiviral interferon response."]},{"key":"dc:format","label":"Dc Format","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["Investigating Interferon-Inducible Antiviral Effectors Through a Virological and Evolutionary Lens"]}]}],"canonical_facts":{"dc:contributor":["Gammon, Don B.","Pfeiffer, Julie K.","Orchard, Robert C.","Schoggins, John W."],"dc:creator":["McDougal, Matthew Bret"],"dc:date":["2026-06-15T19:42:10Z","2024-05","May 2024","2026-06-15T19:42:11Z"],"dc:description":["Interferons control viral infection by inducing expression of effector proteins encoded by interferon-stimulated genes (ISGs). The field has focused on identifying antiviral ISG effectors and defining their mechanisms of action. However, fundamental gaps in knowledge about the interferon response remain. For example, it is unknown how many ISGs are required to restrict a particular virus, though it is theorized that numerous ISGs act in concert to achieve viral inhibition. Here, I used CRISPR-based loss-of-function screens to identify a limited set of ISGs that confer interferon-mediated suppression of Venezuelan equine encephalitis virus (VEEV). I show via combinatorial gene targeting that antiviral effectors - ZAP, IFIT3, and IFIT1 - together constitute the majority of interferon-mediated VEEV restriction, while comprising less than 0.5% of the interferon-induced transcriptome. Together, my data suggest a refined model of the antiviral interferon response in which a small subset of "dominant" ISGs may confer the bulk of the inhibition of a given virus. One of these "dominant" ISGs, IFIT1, recognizes and binds to RNAs lacking the 5' features of host mRNAs, resulting in targeted suppression of viral RNA translation. This interaction creates significant host-driven evolutionary pressure, as many viruses have evolved mechanisms to evade IFIT1 antiviral function. However, less is known about the virus-driven pressures that have shaped the antiviral activity of mammalian IFIT1 genes. Here, I used evolutionary approaches to show that the IFIT1 gene is rapidly evolving in multiple mammalian orders, with positive selection acting upon several residues in distinct regions of the protein. In functional assays with IFIT1s spanning diverse mammals, I show that IFIT1 exhibits a range of antiviral phenotypes. Some orthologs lack antiviral activity against viruses that are strongly suppressed by others, such as chimpanzee IFIT1, which does not inhibit VEEV infection. I further determine that IFIT1 from human and one species of bat exhibit potent anti-VEEV activity and strong affinity for VEEV Cap0 RNA, while IFIT1 from chimpanzee does not. Using targeted mutagenesis, I identify residues responsible for chimpanzee IFIT1 loss of anti-VEEV function, some of which are rapidly evolving. Together, my studies provide insight into the influence of evolution on IFIT1 antiviral activity and the antiviral interferon response."],"dc:format":["application/pdf"],"dc:identifier":["https://hdl.handle.net/2152.5/10802","1596185280"],"dc:language":["en"],"dc:subject":["Adaptor Proteins, Signal Transducing","Encephalitis Virus, Venezuelan Equine","Evolution, Molecular","RNA-Binding Proteins","Virus Diseases","Viruses"],"dc:title":["Investigating Interferon-Inducible Antiviral Effectors Through a Virological and Evolutionary Lens"],"dc:type":["Thesis","text"]},"updated_at":"2026-07-24T05:52:31Z"}