Global Phosphoproteomics Analysis of IBRS-2 Cells Infected With Senecavirus A
Phosphorylation is a widespread posttranslational modification that regulates numerous biological processes. Viruses can alter the physiological activities of host cells to promote virus particle replication, and manipulating phosphorylation is one of the mechanisms. Senecavirus A (SVA) is the causa...
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Frontiers Media S.A.
2022-01-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2022.832275/full |
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| author | Jieyi Li Zhongwang Zhang Zhongwang Zhang Jianliang Lv Jianliang Lv Zhongyuan Ma Li Pan Li Pan Yongguang Zhang Yongguang Zhang |
| author_facet | Jieyi Li Zhongwang Zhang Zhongwang Zhang Jianliang Lv Jianliang Lv Zhongyuan Ma Li Pan Li Pan Yongguang Zhang Yongguang Zhang |
| author_sort | Jieyi Li |
| collection | DOAJ |
| description | Phosphorylation is a widespread posttranslational modification that regulates numerous biological processes. Viruses can alter the physiological activities of host cells to promote virus particle replication, and manipulating phosphorylation is one of the mechanisms. Senecavirus A (SVA) is the causative agent of porcine idiopathic vesicular disease. Although numerous studies on SVA have been performed, comprehensive phosphoproteomics analysis of SVA infection is lacking. The present study performed a quantitative mass spectrometry-based phosphoproteomics survey of SVA infection in Instituto Biologico-Rim Suino-2 (IBRS-2) cells. Three parallel experiments were performed, and 4,520 phosphosites were quantified on 2,084 proteins. Gene Ontology (GO) functional enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses showed that many phosphorylated proteins were involved in apoptosis and spliceosome pathways, and subcellular structure localization analysis revealed that more than half were located in the nucleus. Motif analysis of proteins with differentially regulated phosphosites showed that proline, aspartic acid, and glutamic acid were the most abundant residues in the serine motif, while proline and arginine were the most abundant in the threonine motif. Forty phosphosites on 27 proteins were validated by parallel reaction monitoring (PRM) phosphoproteomics, and 30 phosphosites in 21 proteins were verified. Nine proteins with significantly altered phosphosites were further discussed, and eight [SRRM2, CDK13, DDX20, DDX21, BAD, ELAVL1, PDZ-binding kinase (PBK), and STAT3] may play a role in SVA infection. Finally, kinase activity prediction showed 10 kinases’ activity was reversed following SVA infection. It is the first phosphoproteomics analysis of SVA infection of IBRS-2 cells, and the results greatly expand our knowledge of SVA infection. The findings provide a basis for studying the interactions of other picornaviruses and their mammalian host cells. |
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| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-12-20T10:22:34Z |
| publishDate | 2022-01-01 |
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| series | Frontiers in Microbiology |
| spelling | doaj.art-cdfe4f7d3c3c4a7ab1c2fda79fe8d15f2022-12-21T19:43:53ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2022-01-011310.3389/fmicb.2022.832275832275Global Phosphoproteomics Analysis of IBRS-2 Cells Infected With Senecavirus AJieyi Li0Zhongwang Zhang1Zhongwang Zhang2Jianliang Lv3Jianliang Lv4Zhongyuan Ma5Li Pan6Li Pan7Yongguang Zhang8Yongguang Zhang9State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, ChinaState Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, ChinaJiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, ChinaState Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, ChinaJiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, ChinaState Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, ChinaState Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, ChinaJiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, ChinaState Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, ChinaLanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Beijing, ChinaPhosphorylation is a widespread posttranslational modification that regulates numerous biological processes. Viruses can alter the physiological activities of host cells to promote virus particle replication, and manipulating phosphorylation is one of the mechanisms. Senecavirus A (SVA) is the causative agent of porcine idiopathic vesicular disease. Although numerous studies on SVA have been performed, comprehensive phosphoproteomics analysis of SVA infection is lacking. The present study performed a quantitative mass spectrometry-based phosphoproteomics survey of SVA infection in Instituto Biologico-Rim Suino-2 (IBRS-2) cells. Three parallel experiments were performed, and 4,520 phosphosites were quantified on 2,084 proteins. Gene Ontology (GO) functional enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses showed that many phosphorylated proteins were involved in apoptosis and spliceosome pathways, and subcellular structure localization analysis revealed that more than half were located in the nucleus. Motif analysis of proteins with differentially regulated phosphosites showed that proline, aspartic acid, and glutamic acid were the most abundant residues in the serine motif, while proline and arginine were the most abundant in the threonine motif. Forty phosphosites on 27 proteins were validated by parallel reaction monitoring (PRM) phosphoproteomics, and 30 phosphosites in 21 proteins were verified. Nine proteins with significantly altered phosphosites were further discussed, and eight [SRRM2, CDK13, DDX20, DDX21, BAD, ELAVL1, PDZ-binding kinase (PBK), and STAT3] may play a role in SVA infection. Finally, kinase activity prediction showed 10 kinases’ activity was reversed following SVA infection. It is the first phosphoproteomics analysis of SVA infection of IBRS-2 cells, and the results greatly expand our knowledge of SVA infection. The findings provide a basis for studying the interactions of other picornaviruses and their mammalian host cells.https://www.frontiersin.org/articles/10.3389/fmicb.2022.832275/fullprotein modificationphosphoproteomebioinformaticsSenecavirus Apathway analysis |
| spellingShingle | Jieyi Li Zhongwang Zhang Zhongwang Zhang Jianliang Lv Jianliang Lv Zhongyuan Ma Li Pan Li Pan Yongguang Zhang Yongguang Zhang Global Phosphoproteomics Analysis of IBRS-2 Cells Infected With Senecavirus A Frontiers in Microbiology protein modification phosphoproteome bioinformatics Senecavirus A pathway analysis |
| title | Global Phosphoproteomics Analysis of IBRS-2 Cells Infected With Senecavirus A |
| title_full | Global Phosphoproteomics Analysis of IBRS-2 Cells Infected With Senecavirus A |
| title_fullStr | Global Phosphoproteomics Analysis of IBRS-2 Cells Infected With Senecavirus A |
| title_full_unstemmed | Global Phosphoproteomics Analysis of IBRS-2 Cells Infected With Senecavirus A |
| title_short | Global Phosphoproteomics Analysis of IBRS-2 Cells Infected With Senecavirus A |
| title_sort | global phosphoproteomics analysis of ibrs 2 cells infected with senecavirus a |
| topic | protein modification phosphoproteome bioinformatics Senecavirus A pathway analysis |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2022.832275/full |
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