Structural characterization of the Human Endogenous Retrovirus and SARS-CoV-2
<p>Retroviruses, a type of RNA virus, have a unique life cycle wherein they reverse transcribe their viral RNA genome and integrate as a provirus into the host’s DNA. When retroviruses integrate into the germ line of humans, they can form human endogenous retroviruses (HERVs), which make up ap...
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| Format: | Thesis |
| Language: | English |
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2023
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| _version_ | 1826312185552306176 |
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| author | Krebs, AS |
| author2 | Zhang, P |
| author_facet | Zhang, P Krebs, AS |
| author_sort | Krebs, AS |
| collection | OXFORD |
| description | <p>Retroviruses, a type of RNA virus, have a unique life cycle wherein they reverse transcribe their viral RNA genome and integrate as a provirus into the host’s DNA. When retroviruses integrate into the germ line of humans, they can form human endogenous retroviruses (HERVs), which make up approximately 8% of the human genome. HERV-K (HML-2) is the most recently acquired HERV but mutations have rendered it mostly silent except in many cancers, neurological diseases, and during the aging process. </p>
<p>To better understand HERV-K, I expressed its main structural protein Gag and determined its structure in the immature CA lattice of virus-like particles (VLPs). HERV-K VLPs have a greater distance between the membrane and the immature capsid (CA) lattice than other retroviruses, which correlates with the presence of small proteins SP1 and p15 between CA and MA. Using cryo-electron tomography (cryoET) and subtomogram averaging (STA), we resolved the immature lattice of HERV-K CA to 3.2A. The resulting map allowed me to build a hexameric atomic model with most side chains well resolved. I confirmed the trimeric and dimeric interactions between hexamers using site-directed mutagenesis and molecular dynamics simulations. A large conformational change in the lattice must occur during maturation, which is driven by the linker between the N-terminal and C-terminal domain, similar to HIV-1. A structure-based phylogenetic analysis with corresponding CA structures of other retroviruses revealed highly conserved assembly patterns across genera and evolutionary time. </p>
<p>SARS-CoV-2, another RNA virus, caused a worldwide pandemic in 2020. We analyzed the structure of the spike (S) protein derived from the ChAdOx1 nCoV-19 vaccine using subtomogram averaging. We found S to be in its prefusion conformation, which can elicit an immune response for protection. We also used a multimodal, multiscalar approach of frozen, infected cells to study assembly and egress of SARS-CoV-2. Our approach can now be applied to a wide range of viruses to understand different viral life cycles.</p> |
| first_indexed | 2024-03-07T08:23:44Z |
| format | Thesis |
| id | oxford-uuid:ccd15eb0-5d23-42c5-8df7-f4e4d4576f0e |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T08:23:44Z |
| publishDate | 2023 |
| record_format | dspace |
| spelling | oxford-uuid:ccd15eb0-5d23-42c5-8df7-f4e4d4576f0e2024-02-07T10:38:57ZStructural characterization of the Human Endogenous Retrovirus and SARS-CoV-2Thesishttp://purl.org/coar/resource_type/c_db06uuid:ccd15eb0-5d23-42c5-8df7-f4e4d4576f0eCOVID-19 (Disease)Retrovirus infectionsVirus diseasesEnglishHyrax Deposit2023Krebs, ASZhang, PBowden, T<p>Retroviruses, a type of RNA virus, have a unique life cycle wherein they reverse transcribe their viral RNA genome and integrate as a provirus into the host’s DNA. When retroviruses integrate into the germ line of humans, they can form human endogenous retroviruses (HERVs), which make up approximately 8% of the human genome. HERV-K (HML-2) is the most recently acquired HERV but mutations have rendered it mostly silent except in many cancers, neurological diseases, and during the aging process. </p> <p>To better understand HERV-K, I expressed its main structural protein Gag and determined its structure in the immature CA lattice of virus-like particles (VLPs). HERV-K VLPs have a greater distance between the membrane and the immature capsid (CA) lattice than other retroviruses, which correlates with the presence of small proteins SP1 and p15 between CA and MA. Using cryo-electron tomography (cryoET) and subtomogram averaging (STA), we resolved the immature lattice of HERV-K CA to 3.2A. The resulting map allowed me to build a hexameric atomic model with most side chains well resolved. I confirmed the trimeric and dimeric interactions between hexamers using site-directed mutagenesis and molecular dynamics simulations. A large conformational change in the lattice must occur during maturation, which is driven by the linker between the N-terminal and C-terminal domain, similar to HIV-1. A structure-based phylogenetic analysis with corresponding CA structures of other retroviruses revealed highly conserved assembly patterns across genera and evolutionary time. </p> <p>SARS-CoV-2, another RNA virus, caused a worldwide pandemic in 2020. We analyzed the structure of the spike (S) protein derived from the ChAdOx1 nCoV-19 vaccine using subtomogram averaging. We found S to be in its prefusion conformation, which can elicit an immune response for protection. We also used a multimodal, multiscalar approach of frozen, infected cells to study assembly and egress of SARS-CoV-2. Our approach can now be applied to a wide range of viruses to understand different viral life cycles.</p> |
| spellingShingle | COVID-19 (Disease) Retrovirus infections Virus diseases Krebs, AS Structural characterization of the Human Endogenous Retrovirus and SARS-CoV-2 |
| title | Structural characterization of the Human Endogenous Retrovirus and SARS-CoV-2 |
| title_full | Structural characterization of the Human Endogenous Retrovirus and SARS-CoV-2 |
| title_fullStr | Structural characterization of the Human Endogenous Retrovirus and SARS-CoV-2 |
| title_full_unstemmed | Structural characterization of the Human Endogenous Retrovirus and SARS-CoV-2 |
| title_short | Structural characterization of the Human Endogenous Retrovirus and SARS-CoV-2 |
| title_sort | structural characterization of the human endogenous retrovirus and sars cov 2 |
| topic | COVID-19 (Disease) Retrovirus infections Virus diseases |
| work_keys_str_mv | AT krebsas structuralcharacterizationofthehumanendogenousretrovirusandsarscov2 |