Activation of ATF3 via the Integrated Stress Response Pathway Regulates Innate Immune and Autophagy Processes to Restrict Zika Virus

Abstract

AbstractZika virus (ZIKV) is a re-emerging mosquito-borne flavivirus that can have devastating health consequences. The developmental and neurological effects from a ZIKV infection arise in part from the virus triggering cellular stress pathways and perturbing transcriptional programs. To date, the underlying mechanisms of transcriptional control directing viral restriction and virus-host interaction are understudied. Activating Transcription Factor 3 (ATF3) is a stress-induced transcriptional effector that modulates the expression of genes involved in a myriad of cellular processes, including inflammation and antiviral responses, to restore cellular homeostasis. While ATF3 is known to be upregulated during ZIKV infection, the mode by which ATF3 is activated and the specific role of ATF3 during ZIKV infection is unknown. In this study, we show via inhibitor and RNA interference approaches that ZIKV infection initiates the integrated stress response pathway to activate ATF4 which in turn induces ATF3 expression. Additionally, by using a CRISPR-Cas9 system to deplete ATF3, we found that ATF3 acts to limit ZIKV gene expression in A549 cells. In particular, the ATF3-dependent anti-ZIKV response occurred through regulation of innate immunity and autophagy pathways. We show that ATF3 differentially regulates the expression of innate immune response genes and suppresses the transcription of autophagy related genes to influence autophagic flux. Our study therefore highlights an important role for the integrated stress response pathway and ATF3 in establishing an antiviral effect during ZIKV infection.ImportanceZIKV is a re-emerging mosquito-borne flavivirus associated with congenital Zika syndrome in infants and Guillain Barré syndrome in adults. As a cytoplasmic virus, ZIKV co-opts host cellular mechanisms to support viral processes and consequently, reprograms the host transcriptional profile. Such viral-directed transcriptional changes and their proor anti-viral significance remain understudied. We previously showed that ATF3, a stress-induced transcription factor, is significantly upregulated in ZIKV infected mammalian cells, along with other cellular and immune response genes. Here, we specifically define the intracellular pathway responsible for ATF3 activation and elucidate the impact of ATF3 expression on ZIKV infection. Our data provides novel insights into the role of the integrated stress response pathway in stimulating ATF3 which differentially regulates the innate immune response and autophagy at the transcript level to antagonize ZIKV gene expression. This study establishes a framework that links viral-induced stress response to transcriptional regulation of host defense pathways and thus expands the depth of knowledge on virus-mediated transcriptional mechanisms during ZIKV infection which in turn will inform future therapeutic strategies.