Bacteria–autophagy interplay: a battle for survival

Key Points Autophagy is used by the cell to degrade various substrates; this is achieved either through the canonical, non-selective autophagy pathway or through selective autophagy. Both pathways proceed via distinct key steps and use specific molecular mechanisms. The canonical autophagy pathway has been studied in detail in mammalian cells and in model organisms, such as yeast. The molecular mechanisms underlying non-canonical autophagy, in addition to alternative pathways that are independent of some of the key autophagy machinery, are beginning to become clear. Besides degradation of cellular proteins, autophagy proteins are also involved in many other functions, some of which are important during bacterial infections. Autophagy functions as an antibacterial mechanism. The induction and recognition mechanisms for several bacterial species have been elucidated. Bacteria can escape killing by autophagy and some can even use autophagy to promote infection of host cells, through the interaction between bacterial effector proteins and autophagy components. The knowledge about bacteria–autophagy interactions will inform the design of new drugs and treatments against bacterial infections. Autophagy not only degrades components of host cells but can also target intracellular bacteria and thus contribute to host defences. Here, Huang and Brumell discuss the canonical and selective pathways of antibacterial autophagy, as well as the ways in which bacteria can escape from them and sometimes even use them to promote infection. Autophagy is a cellular process that targets proteins, lipids and organelles to lysosomes for degradation, but it has also been shown to combat infection with various pathogenic bacteria. In turn, bacteria have developed diverse strategies to avoid autophagy by interfering with autophagy signalling or the autophagy machinery and, in some cases, they even exploit autophagy for their growth. In this Review, we discuss canonical and non-canonical autophagy pathways and our current knowledge of antibacterial autophagy, with a focus on the interplay between bacterial factors and autophagy components.