Senecavirus A isolate:SVA-715
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ABSTRACT:
PROVIDER: PRJNA353236 | ENA |
REPOSITORIES: ENA
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Project description:Senecavirus A strain:SVA/MN/US/2015 Genome sequencing and assembly
| PRJNA553255 | ENA
Project description:Senecavirus A (SVA) belongs to the family of small RNA viruses, the genus Senecavirus, and has become a research hotspot because of the oncolytic viral characteristics. PIWI-interacting RNAs (piRNAs) are a class of small RNAs found in mammalian cells in recent years; however, the host piRNA expression profile during SVA infection and their role in viral infection is not well understood. In this study, we obtained small RNA transcriptome expression profiles from SVA-infected pig kidney cell lines (PK-15) by high-throughput sequencing. Differential expression (DE) analysis, GO annotation, and KEGG analysis of piRNAs in SVA-infected and non-infected PK-15 cells were performed. qRT-PCR was used to validate the DE of piRNAs. The results showed that 981 and 1,370 novel piRNAs were identified in SVA-infected and non-infected PK-15 cells; expression of 129 piRNAs was upregulated while that of 44 piRNAs was downregulated after SVA infection. The DE of 10 piRNAs was further verified by qRT-PCR. GO annotation analysis results showed the metabolism, proliferation, and differentiation were significantly activated after SVA infection. KEGG results showed that after SVA infection, piRNA was mainly enriched in AMPK signaling pathway, Rap1 signaling pathway, circadian rhythm, and VEGF signaling pathway, which suggested that piRNAs may play a role in regulating antiviral immunity, intracellular homeostasis, and tumor processes during SVA infection. This is the first report of the piRNA transcriptome in pig kidney cells and will contribute to the research of piRNA regulatory mechanism during SVA infections and provide an important reference for the prevention and treatment of SVA.
2023-01-05 | GSE222010 | GEO
Project description:Senecavirus A (SVA) belongs to the genus Senecavirus in the family Picornaviridae. It is increasingly used for proteomic research that tandem mass tag-labeled liquid chromatography-tandem mass spectrometry is combined with the parallel reaction monitoring technique. In this study, this combined method was used to uncover separately proteomic profiles of SVA- and non-infected BSR-T7/5 cells. Further, both proteomic profiles were compared with each other. The proteomic profiling showed that a total of 361 differentially expressed proteins were identified, out of which, 305 and 56 were upregulated and downregulated in SVA-infected cells at 12 h post-inoculation, respectively. GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analyses showed that cellular metabolisms were mainly affected in SVA-inoculated cells at an early stage of infection.
2021-09-10 | PXD024947 | Pride
Project description:Phosphorylation is a widespread post-translational 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) the causative agent of porcine idiopathic vesicular disease. Although numerous studies on SVA have been performed, comprehensive phosphoproteomics analysis of SVA infection is lacking. In the present study, we 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 4520 phosphosites were identified on 2084 proteins. Gene Ontology functional enrichment and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses showed that many of the phosphorylated proteins were involved in apoptosis and spliceosome pathways, and subcellular structure localisation 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 phosphoproteomics, and 30 phosphosites in 21 proteins were verified. Nine proteins with significantly altered phosphosites were further explored, and eight (SRRM2, CDK13, DDX20, DDX21, BAD, ELAVL1, PBK, and STAT3) may play a role in SVA infection. Finally, identified eight predicted kinases, and the kinase activity of inhibitor of nuclear factor kappa-B kinase subunit β and CDK9 was reversed following SVA infection. This 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.
2022-02-22 | PXD022444 | Pride
Project description:Phosphorylation is a widespread post-translational 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) the causative agent of porcine idiopathic vesicular disease. Although numerous studies on SVA have been performed, comprehensive phosphoproteomics analysis of SVA infection is lacking. In the present study, we 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 4520 phosphosites were identified on 2084 proteins. Gene Ontology functional enrichment and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses showed that many of the phosphorylated proteins were involved in apoptosis and spliceosome pathways, and subcellular structure localisation 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 phosphoproteomics, and 30 phosphosites in 21 proteins were verified. Nine proteins with significantly altered phosphosites were further explored, and eight (SRRM2, CDK13, DDX20, DDX21, BAD, ELAVL1, PBK, and STAT3) may play a role in SVA infection. Finally, identified eight predicted kinases, and the kinase activity of inhibitor of nuclear factor kappa-B kinase subunit β and CDK9 was reversed following SVA infection. This 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.
2022-02-22 | PXD026655 | Pride
Project description:To investigate the mRNA m6A modification profiling in Mesocricetus auratus cells that infected with Senecavirus, we used passage-5 Senecavirus A to infect BSR-T7/5 cells. We then performed m6A MeRIP-seq(GenSeq®️ m6A MeRIP Kit) at at two time points (12hrs or 72 hrs after infection), each time point with three replicates.
2022-06-30 | GSE206974 | GEO