IFNγ Inhibits the Cytosolic Replication of Shigella flexneri via the Cytoplasmic RNA Sensor RIG-I

The activation of host cells by interferon gamma (IFN gamma) is essential for inhibiting the intracellular replication of most microbial pathogens. Although significant advances have been made in identifying IFN gamma-dependent host factors that suppress intracellular bacteria, little is known about how IFN gamma enables cells to recognize, or restrict, the growth of pathogens that replicate in the host cytoplasm. The replication of the cytosolic bacterial pathogen Shigella flexneri is significantly inhibited in IFN gamma-stimulated cells, however the specific mechanisms that mediate this inhibition have remained elusive. We found that S. flexneri efficiently invades IFN gamma-activated mouse embryonic fibroblasts (MEFs) and escapes from the vacuole, suggesting that IFN gamma acts by blocking S. flexneri replication in the cytosol. This restriction on cytosolic growth was dependent on interferon regulatory factor 1 (IRF1), an IFN gamma-inducible transcription factor capable of inducing IFN gamma-mediated cell-autonomous immunity. To identify host factors that restrict S. flexneri growth, we used whole genome microarrays to identify mammalian genes whose expression in S. flexneri-infected cells is controlled by IFN gamma and IRF1. Among the genes we identified was the pattern recognition receptor (PRR) retanoic acid-inducible gene I (RIG-I), a cytoplasmic sensor of foreign RNA that had not been previously known to play a role in S. flexneri infection. We found that RIG-I and its downstream signaling adaptor mitochondrial antiviral signaling protein (MAVS)-but not cytosolic Nod-like receptors (NLRs)-are critically important for IFN gamma-mediated S. flexneri growth restriction. The recently described RNA polymerase III pathway, which transcribes foreign cytosolic DNA into the RIG-I ligand 5'-triphosphate RNA, appeared to be involved in this restriction. The finding that RIG-I responds to S. flexneri infection during the IFN gamma response extends the range of PRRs that are capable of recognizing this bacterium. Additionally, these findings expand our understanding of how IFN gamma recognizes, and ultimately restricts, bacterial pathogens within host cells.