Autophagy and innate recognition systems

Autophagy is an ancient, highly conserved pathway responsible for the lysosomal degradation of cytosolic constituents and organelles that is critical in maintaining cellular homeostasis. Recent studies have illustrated an important interplay between autophagy and the innate immune system. Signaling through innate pattern recognition receptors leads to the induction of autophagy. Autophagy is utilized by the innate immune cells to survey for virus infection through delivery of cytosolic viral replication complexes to the endosomal viral sensors. In another case, key molecules in the autophagy pathway were found to negatively regulate cytosolic sensors of RNA viruses. Moreover, it has recently become apparent that the autophagic machinery is utilized by phagocytic cells for efficient phagocytosis and clearance of extracellular pathogens. These studies shed light on the possibility that molecules classically thought to be dedicated to the process of autophagy may function in important physiological processes independent of autophagy, whereby the double-membrane structures form within the cytosol to enclose organelles and long-lived proteins. In this chapter, we will highlight key findings relevant to the role of the autophagic machinery in the innate immune system.