Autophagy gene-dependent intracellular immunity triggered by interferon-γ

Genes required for the lysosomal degradation pathway of autophagy play key roles in topologically distinct cellular processes with significant physiologic importance. One of the first-described of these ATG gene-dependent processes is the requirement for a subset of ATG genes in interferon-{gamma} (IFN{gamma})-induced inhibition of norovirus and Toxoplasma gondii replication. Herein we identified new genes that are required for or that negatively regulate this immune mechanism. Enzymes involved in the conjugation of UFM1 to target proteins including UFC1 and UBA5, negatively regulated IFN{gamma}-induced inhibition of norovirus replication via effects of Ern1. IFN{gamma}-induced inhibition of norovirus replication required Wipi2b and Atg9a, but not Becn1 (encoding Beclin1), Atg14, or Sqstm1. The phosphatidylinositol-3-phosphate and ATG16L1 binding domains of WIPI2B were required for IFN{gamma}-induced inhibition of norovirus replication. Both WIPI2 and SQSTM1 were required for IFN{gamma}-induced inhibition of Toxoplasma gondii replication in HeLa cells. These studies further delineate the mechanisms of a programmable form of cytokine-induced intracellular immunity that relies on an expanding cassette of essential ATG genes to restrict the growth of phylogenetically diverse pathogens. ImportanceInterferon-{gamma} is a critical mediator of cell-intrinsic immunity to intracellular pathogens. Understanding the complex cellular mechanisms supporting robust interferon-{gamma}-induced host defenses could aid in developing new therapeutics to treat infections. Here, we examined the impact of autophagy in the interferon-{gamma} induced host response. We demonstrate that CRISPR-Cas9 screens specifically targeting the autophagy pathway uncover a role for WIPI2 in IFN{gamma}-induced inhibition of Norovirus replication in mouse cells and IFN{gamma} mediated restriction of the Toxoplasma gondii parasitophorous vacuole in human cells. Furthermore, we found perturbation of UFMylation pathway components led to more robust IFN{gamma}-induced inhibition of Norovirus due to ER stress in vitro. Enhancing or inhibiting these dynamic cellular components could serve as a strategy to weaken intracellular pathogens and maintain an effective immune response.