UFMylation suppresses Type I IFN signaling during M. tuberculosis infection of human macrophages

Type I Interferons (Type I IFNs) are critical for host defense against a wide range of viral infections but can enhance the pathogenicity of several bacterial pathogens, including Mycobacterium tuberculosis (Mtb)1-4. Given the significance of Type I IFN signaling in determining Mtb infection outcomes we sought to uncover new molecular mechanisms controlling Type I IFN activation during mycobacterial infection. We performed a genome-wide CRISPR interference screen in human macrophages to identify genes that regulate IFN-{beta}, during infection with M. marinum (Mm). In addition to known regulators of Type I IFN, we identified UFL1, which encodes the E3 ligase for the ubiquitin-like protein UFM1, as a major regulator of IFN-{beta} during mycobacterial infection. Depletion of other components of the UFMylation pathway, DDRGK1 and UFM1, also resulted in increased IFN-{beta}, indicating that UFMylation activity is required for Type I IFN regulation. Deficiency in UFMylation resulted in increased production and secretion of IFN-{beta} during macrophage infection with both Mm and Mtb compared to control cells. Additionally, silencing UFL1 resulted in increased expression of several interferon stimulated genes and other pro-inflammatory genes, including TNF and IL-6, at both the mRNA and protein level. Transcriptional profiling revealed a surprisingly broad increase in pro-inflammatory responses of UFL1-deficient cells during Mtb infection, particularly for interferon-stimulated genes. Our data reveals an unexpected role of the UFMylation pathway in suppressing Type I IFN, a pro-inflammatory immune pathway with detrimental effects on Mtb infection outcome.