High-sensitivity profiling of SARS-CoV-2 noncoding region–host protein interactome reveals the potential regulatory role of negative-sense viral RNA
ABSTRACT A deep understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)–host interactions is crucial to developing effective therapeutics and addressing the threat of emerging coronaviruses. The role of noncoding regions of viral RNA (ncrRNAs) has yet to be systematically scrut...
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| Format: | Article |
| Language: | English |
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American Society for Microbiology
2023-08-01
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| Series: | mSystems |
| Subjects: | |
| Online Access: | https://journals.asm.org/doi/10.1128/msystems.00135-23 |
| _version_ | 1797730319231614976 |
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| author | Liuyiqi Jiang Mu Xiao Qing-Qing Liao Luqian Zheng Chunyan Li Yuemei Liu Bing Yang Aiming Ren Chao Jiang Xin-Hua Feng |
| author_facet | Liuyiqi Jiang Mu Xiao Qing-Qing Liao Luqian Zheng Chunyan Li Yuemei Liu Bing Yang Aiming Ren Chao Jiang Xin-Hua Feng |
| author_sort | Liuyiqi Jiang |
| collection | DOAJ |
| description | ABSTRACT A deep understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)–host interactions is crucial to developing effective therapeutics and addressing the threat of emerging coronaviruses. The role of noncoding regions of viral RNA (ncrRNAs) has yet to be systematically scrutinized. We developed a method using MS2 affinity purification coupled with liquid chromatography-mass spectrometry and designed a diverse set of bait ncrRNAs to systematically map the interactome of SARS-CoV-2 ncrRNA in Calu-3, Huh7, and HEK293T cells. Integration of the results defined the core ncrRNA–host protein interactomes among cell lines. The 5′ UTR interactome is enriched with proteins in the small nuclear ribonucleoproteins family and is a target for the regulation of viral replication and transcription. The 3′ UTR interactome is enriched with proteins involved in the stress granules and heterogeneous nuclear ribonucleoproteins family. Intriguingly, compared with the positive-sense ncrRNAs, the negative-sense ncrRNAs, especially the negative-sense of 3′ UTR, interacted with a large array of host proteins across all cell lines. These proteins are involved in the regulation of the viral production process, host cell apoptosis, and immune response. Taken together, our study depicts the comprehensive landscape of the SARS-CoV-2 ncrRNA–host protein interactome and unveils the potential regulatory role of the negative-sense ncrRNAs, providing a new perspective on virus–host interactions and the design of future therapeutics. Given the highly conserved nature of UTRs in positive-strand viruses, the regulatory role of negative-sense ncrRNAs should not be exclusive to SARS-CoV-2. IMPORTANCE Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes COVID-19, a pandemic affecting millions of lives. During replication and transcription, noncoding regions of the viral RNA (ncrRNAs) may play an important role in the virus–host interactions. Understanding which and how these ncrRNAs interact with host proteins is crucial for understanding the mechanism of SARS-CoV-2 pathogenesis. We developed the MS2 affinity purification coupled with liquid chromatography-mass spectrometry method and designed a diverse set of ncrRNAs to identify the SARS-CoV-2 ncrRNA interactome comprehensively in different cell lines and found that the 5′ UTR binds to proteins involved in U1 small nuclear ribonucleoprotein, while the 3′ UTR interacts with proteins involved in stress granules and the heterogeneous nuclear ribonucleoprotein family. Interestingly, negative-sense ncrRNAs showed interactions with a large number of diverse host proteins, indicating a crucial role in infection. The results demonstrate that ncrRNAs could serve diverse regulatory functions. |
| first_indexed | 2024-03-12T11:42:35Z |
| format | Article |
| id | doaj.art-6e28dc54e1d14d8e88e94493c49c15a8 |
| institution | Directory Open Access Journal |
| issn | 2379-5077 |
| language | English |
| last_indexed | 2024-03-12T11:42:35Z |
| publishDate | 2023-08-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | mSystems |
| spelling | doaj.art-6e28dc54e1d14d8e88e94493c49c15a82023-08-31T13:00:43ZengAmerican Society for MicrobiologymSystems2379-50772023-08-018410.1128/msystems.00135-23High-sensitivity profiling of SARS-CoV-2 noncoding region–host protein interactome reveals the potential regulatory role of negative-sense viral RNALiuyiqi Jiang0Mu Xiao1Qing-Qing Liao2Luqian Zheng3Chunyan Li4Yuemei Liu5Bing Yang6Aiming Ren7Chao Jiang8Xin-Hua Feng9Life Sciences Institute, Zhejiang University , Hangzhou, Zhejiang, ChinaLife Sciences Institute, Zhejiang University , Hangzhou, Zhejiang, ChinaLife Sciences Institute, Zhejiang University , Hangzhou, Zhejiang, ChinaLife Sciences Institute, Zhejiang University , Hangzhou, Zhejiang, ChinaLife Sciences Institute, Zhejiang University , Hangzhou, Zhejiang, ChinaLife Sciences Institute, Zhejiang University , Hangzhou, Zhejiang, ChinaLife Sciences Institute, Zhejiang University , Hangzhou, Zhejiang, ChinaLife Sciences Institute, Zhejiang University , Hangzhou, Zhejiang, ChinaLife Sciences Institute, Zhejiang University , Hangzhou, Zhejiang, ChinaLife Sciences Institute, Zhejiang University , Hangzhou, Zhejiang, ChinaABSTRACT A deep understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)–host interactions is crucial to developing effective therapeutics and addressing the threat of emerging coronaviruses. The role of noncoding regions of viral RNA (ncrRNAs) has yet to be systematically scrutinized. We developed a method using MS2 affinity purification coupled with liquid chromatography-mass spectrometry and designed a diverse set of bait ncrRNAs to systematically map the interactome of SARS-CoV-2 ncrRNA in Calu-3, Huh7, and HEK293T cells. Integration of the results defined the core ncrRNA–host protein interactomes among cell lines. The 5′ UTR interactome is enriched with proteins in the small nuclear ribonucleoproteins family and is a target for the regulation of viral replication and transcription. The 3′ UTR interactome is enriched with proteins involved in the stress granules and heterogeneous nuclear ribonucleoproteins family. Intriguingly, compared with the positive-sense ncrRNAs, the negative-sense ncrRNAs, especially the negative-sense of 3′ UTR, interacted with a large array of host proteins across all cell lines. These proteins are involved in the regulation of the viral production process, host cell apoptosis, and immune response. Taken together, our study depicts the comprehensive landscape of the SARS-CoV-2 ncrRNA–host protein interactome and unveils the potential regulatory role of the negative-sense ncrRNAs, providing a new perspective on virus–host interactions and the design of future therapeutics. Given the highly conserved nature of UTRs in positive-strand viruses, the regulatory role of negative-sense ncrRNAs should not be exclusive to SARS-CoV-2. IMPORTANCE Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes COVID-19, a pandemic affecting millions of lives. During replication and transcription, noncoding regions of the viral RNA (ncrRNAs) may play an important role in the virus–host interactions. Understanding which and how these ncrRNAs interact with host proteins is crucial for understanding the mechanism of SARS-CoV-2 pathogenesis. We developed the MS2 affinity purification coupled with liquid chromatography-mass spectrometry method and designed a diverse set of ncrRNAs to identify the SARS-CoV-2 ncrRNA interactome comprehensively in different cell lines and found that the 5′ UTR binds to proteins involved in U1 small nuclear ribonucleoprotein, while the 3′ UTR interacts with proteins involved in stress granules and the heterogeneous nuclear ribonucleoprotein family. Interestingly, negative-sense ncrRNAs showed interactions with a large number of diverse host proteins, indicating a crucial role in infection. The results demonstrate that ncrRNAs could serve diverse regulatory functions.https://journals.asm.org/doi/10.1128/msystems.00135-23SARS-CoV-2noncoding region RNAncrRNA-host protein interactions |
| spellingShingle | Liuyiqi Jiang Mu Xiao Qing-Qing Liao Luqian Zheng Chunyan Li Yuemei Liu Bing Yang Aiming Ren Chao Jiang Xin-Hua Feng High-sensitivity profiling of SARS-CoV-2 noncoding region–host protein interactome reveals the potential regulatory role of negative-sense viral RNA mSystems SARS-CoV-2 noncoding region RNA ncrRNA-host protein interactions |
| title | High-sensitivity profiling of SARS-CoV-2 noncoding region–host protein interactome reveals the potential regulatory role of negative-sense viral RNA |
| title_full | High-sensitivity profiling of SARS-CoV-2 noncoding region–host protein interactome reveals the potential regulatory role of negative-sense viral RNA |
| title_fullStr | High-sensitivity profiling of SARS-CoV-2 noncoding region–host protein interactome reveals the potential regulatory role of negative-sense viral RNA |
| title_full_unstemmed | High-sensitivity profiling of SARS-CoV-2 noncoding region–host protein interactome reveals the potential regulatory role of negative-sense viral RNA |
| title_short | High-sensitivity profiling of SARS-CoV-2 noncoding region–host protein interactome reveals the potential regulatory role of negative-sense viral RNA |
| title_sort | high sensitivity profiling of sars cov 2 noncoding region host protein interactome reveals the potential regulatory role of negative sense viral rna |
| topic | SARS-CoV-2 noncoding region RNA ncrRNA-host protein interactions |
| url | https://journals.asm.org/doi/10.1128/msystems.00135-23 |
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