Nonclassical autophagy activation pathways are essential for production of infectious Influenza A virus in vitro

• Published in: Molecular microbiology Vol. 117; no. 2; pp. 508 - 524
• Main Authors: Bell, Tisza A. S., Velappan, Nileena, Gleasner, Cheryl D., Xie, Gang, Starkenburg, Shawn R., Waldo, Geoffrey, Banerjee, Shounak, Micheva‐Viteva, Sofiya N.
• Format: Journal Article
• Language: English
• Published: England Blackwell Publishing Ltd 01.02.2022; Wiley; John Wiley and Sons Inc
• Subjects: Antiinfectives and antibacterials; Autophagy; BASIC BIOLOGICAL SCIENCES; Cancer; Cellular stress response; Epithelial cells; Epithelium; Gene expression; Infections; infectious particles; Influenza; Influenza A; Influenza A virus; Kinases; Lung carcinoma; Mammalian cells; mechanistic target of rapamycin complex 1 (mTORC1); meta-transcriptome; Pandemics; Protein kinase; Replication; RNA-seq; Signaling; Stress analysis; stress‐activated protein kinase (SAPK/JNK); Transcriptomes; ULK1 signaling; Viral infections; Viruses; infectious particles; autophagy; Influenza A virus; RNA-seq; ULK1 signaling; meta-transcriptome; stress-activated protein kinase (SAPK/JNK); mechanistic target of rapamycin complex 1 (mTORC1)
• ISSN: 0950-382X; 1365-2958
• DOI: 10.1111/mmi.14865

Autophagy is a critical mechanism deployed by eukaryotic cells in response to stress, including viral infection, to boost the innate antimicrobial responses. However, an increasing number of pathogens hijack the autophagic machinery to facilitate their own replication. Influenza A virus (IAV), responsible for several global pandemics, has an intricate dependence on autophagy for successful replication in mammalian cells. To elucidate key chokepoints in the host stress responses facilitating IAV replication, we constructed a meta‐transcriptome of IAV and host gene expression dynamics during early (1–3 hpi), mid (4–6 hpi), and late (8–12 hpi) stages of the viral replication cycle at two multiplicities of infection (MOI): 1 and 5. We supplemented the global transcriptome study with phosphoproteomic analysis of stress‐activated protein kinase (SAPK/JNK) signaling in lung carcinoma (predominantly used as an in vitro model of IAV replication) and normal human bronchial epithelial cells. We report significant differences in the activation profiles of autophagy regulating genes upon IAV infection at the two MOI as well as divergent dependence on ULK1 signaling within the normal and cancer cells. Regardless of the cell model, JNK‐Thr187 signaling was crucial for the production of infectious viral particles. Genes regulating mTORC1 and ULK1 signaling pathways are simultaneously activated in Influenza A‐infected lung bronchial epithelium cells. The virus load significantly affects the gene expression dynamics of mTORC1. Stress‐activated protein kinase (SAPK/JNK) signaling is triggered upon accumulation of high levels of viral proteins and coincides with the activation of autophagy.