Unveiling the role of PUS7-mediated pseudouridylation in host protein interactions specific for the SARS-CoV-2 RNA genome
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a positive single-stranded RNA virus, engages in complex interactions with host cell proteins throughout its life cycle. While these interactions enable the host to recognize and inhibit viral replication, they also facilitate essential v...
| Main Authors: | , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2023-12-01
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| Series: | Molecular Therapy: Nucleic Acids |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2162253123002706 |
| _version_ | 1797648367021457408 |
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| author | Roberto Giambruno Elsa Zacco Camilla Ugolini Andrea Vandelli Logan Mulroney Manfredi D’Onghia Bianca Giuliani Elena Criscuolo Matteo Castelli Nicola Clementi Massimo Clementi Nicasio Mancini Tiziana Bonaldi Stefano Gustincich Tommaso Leonardi Gian Gaetano Tartaglia Francesco Nicassio |
| author_facet | Roberto Giambruno Elsa Zacco Camilla Ugolini Andrea Vandelli Logan Mulroney Manfredi D’Onghia Bianca Giuliani Elena Criscuolo Matteo Castelli Nicola Clementi Massimo Clementi Nicasio Mancini Tiziana Bonaldi Stefano Gustincich Tommaso Leonardi Gian Gaetano Tartaglia Francesco Nicassio |
| author_sort | Roberto Giambruno |
| collection | DOAJ |
| description | Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a positive single-stranded RNA virus, engages in complex interactions with host cell proteins throughout its life cycle. While these interactions enable the host to recognize and inhibit viral replication, they also facilitate essential viral processes such as transcription, translation, and replication. Many aspects of these virus-host interactions remain poorly understood. Here, we employed the catRAPID algorithm and utilized the RNA-protein interaction detection coupled with mass spectrometry technology to predict and validate the host proteins that specifically bind to the highly structured 5′ and 3′ terminal regions of the SARS-CoV-2 RNA. Among the interactions identified, we prioritized pseudouridine synthase PUS7, which binds to both ends of the viral RNA. Using nanopore direct RNA sequencing, we discovered that the viral RNA undergoes extensive post-transcriptional modifications. Modified consensus regions for PUS7 were identified at both terminal regions of the SARS-CoV-2 RNA, including one in the viral transcription regulatory sequence leader. Collectively, our findings offer insights into host protein interactions with the SARS-CoV-2 UTRs and highlight the likely significance of pseudouridine synthases and other post-transcriptional modifications in the viral life cycle. This new knowledge enhances our understanding of virus-host dynamics and could inform the development of targeted therapeutic strategies. |
| first_indexed | 2024-03-11T15:31:13Z |
| format | Article |
| id | doaj.art-6eb7df49e017486c8f0fe36a0099dc99 |
| institution | Directory Open Access Journal |
| issn | 2162-2531 |
| language | English |
| last_indexed | 2024-03-11T15:31:13Z |
| publishDate | 2023-12-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Molecular Therapy: Nucleic Acids |
| spelling | doaj.art-6eb7df49e017486c8f0fe36a0099dc992023-10-27T04:24:04ZengElsevierMolecular Therapy: Nucleic Acids2162-25312023-12-0134102052Unveiling the role of PUS7-mediated pseudouridylation in host protein interactions specific for the SARS-CoV-2 RNA genomeRoberto Giambruno0Elsa Zacco1Camilla Ugolini2Andrea Vandelli3Logan Mulroney4Manfredi D’Onghia5Bianca Giuliani6Elena Criscuolo7Matteo Castelli8Nicola Clementi9Massimo Clementi10Nicasio Mancini11Tiziana Bonaldi12Stefano Gustincich13Tommaso Leonardi14Gian Gaetano Tartaglia15Francesco Nicassio16Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, 20139 Milano, Italy; Institute of Biomedical Technologies, National Research Council, 20090 Segrate, Italy; Corresponding author: Roberto Giambruno, Institute of Biomedical Technologies, National Research Council, 20090 Segrate, Italy.Central RNA and RNA Systems Biology Labs, Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), 16152 Genova, ItalyCenter for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, 20139 Milano, Italy; Department of Oncology and Hematology-Oncology, University of Milan, 20122 Milano, ItalyCentral RNA and RNA Systems Biology Labs, Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), 16152 Genova, Italy; Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, SpainCenter for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, 20139 Milano, Italy; European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridgeshire CB10 1SD, UK; Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory (EMBL), Monterotondo, RM 00015, ItalyCenter for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, 20139 Milano, ItalyCenter for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, 20139 Milano, ItalyLaboratory of Microbiology and Virology, Vita-Salute San Raffaele University, 20132 Milan, ItalyLaboratory of Microbiology and Virology, Vita-Salute San Raffaele University, 20132 Milan, ItalyLaboratory of Microbiology and Virology, Vita-Salute San Raffaele University, 20132 Milan, Italy; Laboratory of Medical Microbiology and Virology, IRCCS San Raffaele Scientific Institute, 20132 Milan, ItalyLaboratory of Microbiology and Virology, Vita-Salute San Raffaele University, 20132 Milan, Italy; Laboratory of Medical Microbiology and Virology, IRCCS San Raffaele Scientific Institute, 20132 Milan, ItalyLaboratory of Microbiology and Virology, Vita-Salute San Raffaele University, 20132 Milan, Italy; Laboratory of Medical Microbiology and Virology, IRCCS San Raffaele Scientific Institute, 20132 Milan, ItalyDepartment of Experimental Oncology, European Institute of Oncology IRCCS, 20139 Milano, Italy; Department of Oncology and Hematology-Oncology, University of Milan, 20122 Milano, ItalyCentral RNA and RNA Systems Biology Labs, Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), 16152 Genova, ItalyCenter for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, 20139 Milano, ItalyCentral RNA and RNA Systems Biology Labs, Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), 16152 Genova, Italy; Catalan Institution for Research and Advanced Studies, ICREA, 08010 Barcelona, Spain; Corresponding author: Gian Gaetano Tartaglia, RNA Systems Biology Lab, Istituto Italiano di Tecnologia (IIT), 16152 Genova, Italy.Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, 20139 Milano, Italy; Corresponding author: Francesco Nicassio, Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, 20139 Milano, Italy.Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a positive single-stranded RNA virus, engages in complex interactions with host cell proteins throughout its life cycle. While these interactions enable the host to recognize and inhibit viral replication, they also facilitate essential viral processes such as transcription, translation, and replication. Many aspects of these virus-host interactions remain poorly understood. Here, we employed the catRAPID algorithm and utilized the RNA-protein interaction detection coupled with mass spectrometry technology to predict and validate the host proteins that specifically bind to the highly structured 5′ and 3′ terminal regions of the SARS-CoV-2 RNA. Among the interactions identified, we prioritized pseudouridine synthase PUS7, which binds to both ends of the viral RNA. Using nanopore direct RNA sequencing, we discovered that the viral RNA undergoes extensive post-transcriptional modifications. Modified consensus regions for PUS7 were identified at both terminal regions of the SARS-CoV-2 RNA, including one in the viral transcription regulatory sequence leader. Collectively, our findings offer insights into host protein interactions with the SARS-CoV-2 UTRs and highlight the likely significance of pseudouridine synthases and other post-transcriptional modifications in the viral life cycle. This new knowledge enhances our understanding of virus-host dynamics and could inform the development of targeted therapeutic strategies.http://www.sciencedirect.com/science/article/pii/S2162253123002706MT: RNA/DNA editingprotein-RNA interactionsSARS-CoV-2pseudouridinePUS7proximity biotinylation |
| spellingShingle | Roberto Giambruno Elsa Zacco Camilla Ugolini Andrea Vandelli Logan Mulroney Manfredi D’Onghia Bianca Giuliani Elena Criscuolo Matteo Castelli Nicola Clementi Massimo Clementi Nicasio Mancini Tiziana Bonaldi Stefano Gustincich Tommaso Leonardi Gian Gaetano Tartaglia Francesco Nicassio Unveiling the role of PUS7-mediated pseudouridylation in host protein interactions specific for the SARS-CoV-2 RNA genome Molecular Therapy: Nucleic Acids MT: RNA/DNA editing protein-RNA interactions SARS-CoV-2 pseudouridine PUS7 proximity biotinylation |
| title | Unveiling the role of PUS7-mediated pseudouridylation in host protein interactions specific for the SARS-CoV-2 RNA genome |
| title_full | Unveiling the role of PUS7-mediated pseudouridylation in host protein interactions specific for the SARS-CoV-2 RNA genome |
| title_fullStr | Unveiling the role of PUS7-mediated pseudouridylation in host protein interactions specific for the SARS-CoV-2 RNA genome |
| title_full_unstemmed | Unveiling the role of PUS7-mediated pseudouridylation in host protein interactions specific for the SARS-CoV-2 RNA genome |
| title_short | Unveiling the role of PUS7-mediated pseudouridylation in host protein interactions specific for the SARS-CoV-2 RNA genome |
| title_sort | unveiling the role of pus7 mediated pseudouridylation in host protein interactions specific for the sars cov 2 rna genome |
| topic | MT: RNA/DNA editing protein-RNA interactions SARS-CoV-2 pseudouridine PUS7 proximity biotinylation |
| url | http://www.sciencedirect.com/science/article/pii/S2162253123002706 |
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