Stem loop binding protein promotes SARS-CoV-2 replication via -1 programmed ribosomal frameshifting
Abstract The -1 programmed ribosomal frameshifting (-1 PRF) in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is crucial for keeping the balance between pp1a and pp1ab polyproteins. To date, the host factors influencing this process remain poorly understood. Using RNA pull-down assays...
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| Format: | Article |
| Language: | English |
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Nature Publishing Group
2025-06-01
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| Series: | Signal Transduction and Targeted Therapy |
| Online Access: | https://doi.org/10.1038/s41392-025-02277-w |
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| author | Tanxiu Chen Ruimin Zhu Tingfu Du Hao Yang Xintian Zhang Zhixing Wang Yong Zhang Wenqi Quan Bin Yin Yunpeng Liu Shuaiyao Lu Xiaozhong Peng |
| author_facet | Tanxiu Chen Ruimin Zhu Tingfu Du Hao Yang Xintian Zhang Zhixing Wang Yong Zhang Wenqi Quan Bin Yin Yunpeng Liu Shuaiyao Lu Xiaozhong Peng |
| author_sort | Tanxiu Chen |
| collection | DOAJ |
| description | Abstract The -1 programmed ribosomal frameshifting (-1 PRF) in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is crucial for keeping the balance between pp1a and pp1ab polyproteins. To date, the host factors influencing this process remain poorly understood. Using RNA pull-down assays combined with mass spectrometry screening, we discovered five host proteins interacting with -1 PRF RNA, including Stem Loop Binding Protein (SLBP). Our findings revealed that SLBP overexpression enhanced frameshifting and promoted viral replication. Moreover, the interaction between SLBP and -1 PRF RNA was predicted using the PrismNet deep learning tool, which calculated a high binding probability of 0.922. Using Electrophoretic Mobility Shift Assays (EMSAs) and RNA pull down assays, our findings demonstrated SLBP’s direct binding to the SARS-CoV-2 genome, with preferential affinity for the stem loop 3 region of the -1 PRF RNA. Using smFISH assays, we further confirmed their physical colocalization. The role of SLBP in promoting frameshifting was verified using an in vitro translation system. Further investigation showed that SLBP deletions reshaped the host factor pattern around -1 PRF RNA, diminishing interactions with FUBP3 and RPS3A while enhancing RPL10A binding. Together, our findings identify SLBP as a host protein that promotes SARS-CoV-2 frameshifting, highlighting its potential as a druggable target for COVID-19. |
| format | Article |
| id | doaj-art-110b9d3f3e7049b6b49d5559e37f27d8 |
| institution | Kabale University |
| issn | 2059-3635 |
| language | English |
| publishDate | 2025-06-01 |
| publisher | Nature Publishing Group |
| record_format | Article |
| series | Signal Transduction and Targeted Therapy |
| spelling | doaj-art-110b9d3f3e7049b6b49d5559e37f27d82025-08-20T03:45:32ZengNature Publishing GroupSignal Transduction and Targeted Therapy2059-36352025-06-0110111210.1038/s41392-025-02277-wStem loop binding protein promotes SARS-CoV-2 replication via -1 programmed ribosomal frameshiftingTanxiu Chen0Ruimin Zhu1Tingfu Du2Hao Yang3Xintian Zhang4Zhixing Wang5Yong Zhang6Wenqi Quan7Bin Yin8Yunpeng Liu9Shuaiyao Lu10Xiaozhong Peng11State Key Laboratory of Respiratory Health and Multimorbidity, National Center of Technology Innovation for Animal Model, Key Laboratory of Pathogen Infection Prevention and Control (Peking Union Medical College), Ministry of Education, Institute of Laboratory Animal Science, CAMS & PUMCState Key Laboratory of Respiratory Health and Multimorbidity, National Center of Technology Innovation for Animal Model, Key Laboratory of Pathogen Infection Prevention and Control (Peking Union Medical College), Ministry of Education, Institute of Laboratory Animal Science, CAMS & PUMCInstitute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical CollegeInstitute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical CollegeInstitute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical CollegeDepartment of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, CAMS & PUMCInstitute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical CollegeInstitute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical CollegeDepartment of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, CAMS & PUMCState Key Laboratory of Respiratory Health and Multimorbidity, National Center of Technology Innovation for Animal Model, Key Laboratory of Pathogen Infection Prevention and Control (Peking Union Medical College), Ministry of Education, Institute of Laboratory Animal Science, CAMS & PUMCInstitute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical CollegeState Key Laboratory of Respiratory Health and Multimorbidity, National Center of Technology Innovation for Animal Model, Key Laboratory of Pathogen Infection Prevention and Control (Peking Union Medical College), Ministry of Education, Institute of Laboratory Animal Science, CAMS & PUMCAbstract The -1 programmed ribosomal frameshifting (-1 PRF) in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is crucial for keeping the balance between pp1a and pp1ab polyproteins. To date, the host factors influencing this process remain poorly understood. Using RNA pull-down assays combined with mass spectrometry screening, we discovered five host proteins interacting with -1 PRF RNA, including Stem Loop Binding Protein (SLBP). Our findings revealed that SLBP overexpression enhanced frameshifting and promoted viral replication. Moreover, the interaction between SLBP and -1 PRF RNA was predicted using the PrismNet deep learning tool, which calculated a high binding probability of 0.922. Using Electrophoretic Mobility Shift Assays (EMSAs) and RNA pull down assays, our findings demonstrated SLBP’s direct binding to the SARS-CoV-2 genome, with preferential affinity for the stem loop 3 region of the -1 PRF RNA. Using smFISH assays, we further confirmed their physical colocalization. The role of SLBP in promoting frameshifting was verified using an in vitro translation system. Further investigation showed that SLBP deletions reshaped the host factor pattern around -1 PRF RNA, diminishing interactions with FUBP3 and RPS3A while enhancing RPL10A binding. Together, our findings identify SLBP as a host protein that promotes SARS-CoV-2 frameshifting, highlighting its potential as a druggable target for COVID-19.https://doi.org/10.1038/s41392-025-02277-w |
| spellingShingle | Tanxiu Chen Ruimin Zhu Tingfu Du Hao Yang Xintian Zhang Zhixing Wang Yong Zhang Wenqi Quan Bin Yin Yunpeng Liu Shuaiyao Lu Xiaozhong Peng Stem loop binding protein promotes SARS-CoV-2 replication via -1 programmed ribosomal frameshifting Signal Transduction and Targeted Therapy |
| title | Stem loop binding protein promotes SARS-CoV-2 replication via -1 programmed ribosomal frameshifting |
| title_full | Stem loop binding protein promotes SARS-CoV-2 replication via -1 programmed ribosomal frameshifting |
| title_fullStr | Stem loop binding protein promotes SARS-CoV-2 replication via -1 programmed ribosomal frameshifting |
| title_full_unstemmed | Stem loop binding protein promotes SARS-CoV-2 replication via -1 programmed ribosomal frameshifting |
| title_short | Stem loop binding protein promotes SARS-CoV-2 replication via -1 programmed ribosomal frameshifting |
| title_sort | stem loop binding protein promotes sars cov 2 replication via 1 programmed ribosomal frameshifting |
| url | https://doi.org/10.1038/s41392-025-02277-w |
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