br Acknowledgement This work was

Acknowledgement This work was funded by NIH/NINDS grant number NS080967 to C. Waites.
Introduction Macro-autophagy also called autophagy is a conserved pathway for the lysosomal degradation and recycling of intracellular materials. It is instrumental for the homeostasis of cells and tissues at steady state as well as during ZSTK474 to changes in their micro-environment [1], [2]. During autophagy, aggregated or misformed materials, as well as damaged/senescent organelles, are confined within double-membraned vesicles called autophagosomes and directed to degradation through autophagosome fusion with lysosomes. As a consequence, autophagy regulates many biological processes such as metabolism, inflammation or development. Dysfunction of the autophagy pathway is therefore frequently associated with various pathologies including neurodegenerative diseases, cancer, obesity, cardiovascular diseases, inflammatory diseases or autoimmune disorders [3]. Autophagy is also crucial for cellular defense against invading pathogens and the development of appropriate immune responses. The process of degrading invading microorganisms in lysosomes after encapsulation into autophagosomes is named xenophagy [4]. The role of autophagy as an intrinsic cellular defense mechanism is particularly relevant in the case of infection by viruses as these intruders are obligate intracellular parasites whose successful replication requires the hijacking of the cellular machinery. A growing number of observations indicate that the autophagy process itself, as well as the factors involved in the execution of the autophagic program, can exert both anti-viral and pro-viral influences depending on the virus involved, the type of cell infected or the cellular environment. The autophagic resistance to viral intrusion often involves the specific targeting of viral components by specialized factors called autophagy receptors for encapsulation into autophagosomes and degradation. Autophagy factors can also actively participate in other cellular processes to restrain the cycle of the virus and the egress of viral particles. Finally, core autophagy factors and autophagy regulators can contribute to the initiation of both innate and adaptive immune responses to viral infection. That autophagy could contain viral infections was also observed in vivo[5], [6], [7]. Not surprisingly, many viruses have developed means to counteract the anti-viral activity of autophagy during evolution. While some have evolved strategies to simply escape autophagy, others have developed ways to take advantage of the autophagy process to promote their own replication and spread. There exist several extensive reviews on the complex relationship that has evolved between autophagy and viruses at large [8], [9], [10], [11]. The present article more specifically focuses on the virus–autophagy interactions that take place during the early stages of host cell infection. After providing some background on the autophagic process itself and on innate immune mechanisms that can be mobilized upon viral entry, we will consider the impact of virus sensing on the autophagic status of host cells, the early events that can initiate anti-viral autophagy and the link between autophagy and innate immunity signaling. We will next describe how viruses can manipulate the autophagy machinery in order to modulate type I IFN and inflammatory responses, and even recruit host factors to oppose restriction by autophagy. Then, we will consider the possibility that characteristics of viral particles entry might originate from interaction with the autophagy machinery from the cells they were packaged in. Finally, we will propose a few issues with respect to important questions, challenges and future perspectives.
An overview of the autophagy process Several dozens of genes are involved in autophagy (Atg). Under physiological conditions, autophagy is kept under control by mammalian target of rapamycin complex 1 (mTORC1) that interacts with, and inactivates complexes made of ULK1, FIP200 and Atg13 and preempts the growth of membranes areas susceptible to support autophagy initiation (isolation membranes). Such areas can originate from the endoplasmic reticulum (ER), the Golgi apparatus, ER–mitochondria contact sites or endosomes. mTORC1 activity is balanced by the energy sensor AMP-activated protein kinase which can phosphorylate ULK1. Stimuli that perturbate mTORC1 activity lead to autophagy induction through the activation of the class III phosphatidylinositol 3-kinase Vps34 that forms phosphatidylinositol 3-phosphate on lipids. Vps34 associates with BECLIN 1. Other factors such as UVRAG, RUBICON, ATG14L, BIF-1 or AMBRA1 can interact with this complex to modulate its activity depending on the stage it is involved in [12], [13], [14] (Fig. 1). The growing membrane involved in this initiation is called the phagophore whose elongation involves two distinct ubiquitin-like conjugation systems. On the one hand, ATG7 and ATG10 catalyze the association of Atg12 with Atg5 which is joined by ATG16L1 to assemble the ATG16L1–ATG12–ATG5 complex able to bind to the cup-shaped phagophore. On the other hand, ATG4 cleaves the microtubule-associated protein, light chain 3 (LC3) that gets conjugated to phosphatidylethanolamine in the presence of ATG3 and ATG7. This lipidation, which can be assessed by conventional immuno-blotting, corresponds to the conversion of diffuse, soluble LC3 species (LC3I) to LC3 species that localize to the surface of the elongating phagophore (LC3II). Besides factors of the LC3 type, additional factors called GABARAPs can function according to the same principle. Ultimately, the incurved phagophore undergoes closure to form a vesicle delineated by two membranes: the autophagosome. As the anchoring of LC3II is stable, especially onto the inner membrane, it serves as a marker for autophagosome formation which can be monitored microscopically by analyzing the appearance of LC3 positive, punctiforme structures. The next step of the autophagy process involves the fusion of autophagosomes with lysosomal vesicles to form autolysosomes [13], [14]. This step, called maturation, is incompletely characterized and appears to include intermediate stages where autophagosomes often fuse first with endosomes. Maturation can be regulated by a variety of factors including components of the cytoskeleton, Rab GTPases, soluble N-acetylmaleimide-sensitive factor attachment protein receptors (SNARES), endosomal sorting complexes required for transport (ESCRT) components or membrane-tethering factors such as components of the homotypic fusion and vacuole protein sorting (HOPS) complex along with the PLEKHM1 adaptor [15]. Ultimately, the content of autophagosome gets exposed to the acidic microenvironment of lysosomes as well as to their hydrolases leading to degradation and recycling [15], [16]. While autophagy is often thought to be non-selective, for instance, in the case of nutrients deprivation-induced autophagy, the targeting of particular cargoes such as damaged mitochondria (mitophagy) is dependent on the engagement of specialized factors called autophagy receptors (selective autophagy). These receptors bind to their targets by interacting with ubiquitin/Galectin tags and to phagophore-anchored LC3 molecules via LC3-interacting regions. In many instances, the binding to the cargo appears to involve the recognition of ubiquinated tags. Examples of autophagy receptors that mediate selective autophagy include Optineurin, NDP52, p62/SQSTM1, NIX-BNIP3 factors or NBR1 [17]. Interestingly, some of these autophagy receptors, such as NDP52 and Optineurin, also regulate autophagosome maturation to possibly optimize cargoes degradation [18].