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Temporal Proteomic and Phosphoproteomic Analysis of EV-A71-Infected Human Cells

  • Yue Zhao
    Yue Zhao
    College of Biological Sciences, China Agricultural University, Beijing 100193, China
    Proteomics Center, National Institute of Biological Sciences, Beijing 102206, China
    More by Yue Zhao
  • Lin Li
    Lin Li
    Proteomics Center, National Institute of Biological Sciences, Beijing 102206, China
    More by Lin Li
  • Xinhui Wang
    Xinhui Wang
    CAMS Key Laboratory of Synthetic Biology Regulatory Elements, Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, Jiangsu, China
    Suzhou Institute of Systems Medicine, Suzhou 215123, Jiangsu, China
    More by Xinhui Wang
  • Sudan He
    Sudan He
    CAMS Key Laboratory of Synthetic Biology Regulatory Elements, Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, Jiangsu, China
    Suzhou Institute of Systems Medicine, Suzhou 215123, Jiangsu, China
    More by Sudan He
  • Weifeng Shi
    Weifeng Shi
    Department of Laboratory Medicine, The Third Affiliated Hospital of Soochow University, Changzhou 213003, Jiangsu, China
    More by Weifeng Shi
  • , and 
  • She Chen*
    She Chen
    Proteomics Center, National Institute of Biological Sciences, Beijing 102206, China
    Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
    *She Chen. E-mail: [email protected]
    More by She Chen
Cite this: J. Proteome Res. 2022, 21, 10, 2367–2384
Publication Date (Web):September 15, 2022
https://doi.org/10.1021/acs.jproteome.2c00237
Copyright © 2022 American Chemical Society

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    Abstract

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    Human enterovirus A71 (EV-A71), a member of the Picornaviridae family, is one of the main etiological viruses that lead to hand, foot, and mouth disease (HFMD). We utilized a multiplex tandem mass tag-based quantitative proteomic technique to monitor the alternation of the whole cell proteome and phosphoproteome of human rhabdomyosarcoma cells over the course of EV-A71 infection. We successfully quantified more than 7000 host proteins and 17,000 phosphosites, of which 80 proteins and nearly 1700 phosphosites were significantly regulated upon viral infection. We found that Myc proto-oncogene protein level decreased significantly, benefiting EV-A71 replication. Multiple signaling pathways were regulated in phosphorylation events that converge for protein translation, cell cycle control, and cell survival. Numerous host factors targeted by virus proteins are phosphoproteins. These factors are involved in host translational initiation, unfolded protein response, endoplasmic reticulum stress, and stress granule formation, and their phosphorylation may play key roles in the virus life cycle. Notably, we identified three conserved phosphorylation sites on viral polyproteins that have not been previously reported. Our study provides valuable resources for a systematic understanding of the interaction between the host cells and the EV-A71 at the protein and the post-translational level.

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    The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acs.jproteome.2c00237.

    • Figure S1. Pearson correlation and PCA analysis of the proteomes and phosphoproteomes. Figure S2. Density plots of the fold changes of phosphopeptides and unphosphorylated peptides at different infection time points. Figure S3. Upregulated pathways at 12 hpi from the host proteomes by GO enrichment. Figure S4. Downregulated pathways at 12 hpi from the host proteomes by GO enrichment. Figure S5. Temporal profiles of the 22 significantly downregulated proteins during viral infection. Figure S6. Western blot of MYC, AURKA, and 3D protein during EV-A71 infection. Figure S7. Protein complexes with significant phosphorylation changes during viral infection. Figure S8. Kinase motifs of significantly changed phosphosites by motif-x analysis. Figure S9. Predicted host kinases with regulated activities during viral infection. Figure S10. Western blot of phosphorylated MAPK8 and ATF2 during viral infection. Figure S11. Fragmentation spectra of the three phosphopeptides derived from viral polyprotein (PDF)

    • Table S1. Temporal quantification of the proteomes of the EV-A71-infected RD cells. Table S2. Temporal quantification of the phosphoproteomes of the EV-A71-infected RD cells. Table S3. GO enrichment of the significantly regulated phosphosites. Table S4. Reactome analysis of the significantly regulated phosphosites. Table S5. Phosphorylation changes of the regulated protein complexes (XLSX)

    • Western blot images (PDF)

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