REVIEW published: 18 October 2018 doi: 10.3389/fcimb.2018.00362 Autophagy, EVs, and Infections: A Perfect Question for a Perfect Time Michelle L. Pleet 1†, Heather Branscome 1†, Catherine DeMarino 1, Daniel O. Pinto 1, Mohammad Asad Zadeh 1, Myosotys Rodriguez 2, Ilker Kudret Sariyer 3, Nazira El-Hage 2 and Fatah Kashanchi 1* 1 Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, United States, 2 Department of Immunology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, United States, 3 Department of Neuroscience, Center for Neurovirology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, United States Autophagy, a highly conserved process, serves to maintain cellular homeostasis in response to an extensive variety of internal and external stimuli. The classic, or canonical, pathway of autophagy involves the coordinated degradation and recycling of intracellular components and pathogenic material. Proper regulation of autophagy is critical to Edited by: maintain cellular health, as alterations in the autophagy pathway have been linked to the Wenjun Liu, Institute of Microbiology (CAS), China progression of a variety of physiological and pathological conditions in humans, namely Reviewed by: in aging and in viral infection. In addition to its canonical role as a degradative pathway, a Maria Teresa Sanchez-Aparicio, more unconventional and non-degradative role for autophagy has emerged as an area of Icahn School of Medicine at Mount Sinai, United States increasing interest. This process, known as secretory autophagy, is gaining widespread Alan G. Goodman, attention as many viruses are believed to use this pathway as a means to release and Washington State University, spread viral particles. Moreover, secretory autophagy has been found to intersect with United States other intracellular pathways, such as the biogenesis and secretion of extracellular vesicles *Correspondence: Fatah Kashanchi (EVs). Here, we provide a review of the current landscape surrounding both degradative [email protected] autophagy and secretory autophagy in relation to both aging and viral infection. We †These authors have contributed discuss their key features, while describing their interplay with numerous different viruses equally to this work (i.e. hepatitis B and C viruses, Epstein-Barr virus, SV40, herpesviruses, HIV, chikungunya virus, dengue virus, Zika virus, Ebola virus, HTLV, Rift Valley fever virus, poliovirus, and Specialty section: This article was submitted to influenza A virus), and compare secretory autophagy to other pathways of extracellular Virus and Host, vesicle release. Lastly, we highlight the need for, and emphasize the importance of, more a section of the journal thorough methods to study the underlying mechanisms of these pathways to better Frontiers in Cellular and Infection Microbiology advance our understanding of disease progression. Received: 26 June 2018 Keywords: autophagy, exosome, extracellular vesicle, virus, infectious disease, secretory autophagy Accepted: 28 September 2018 Published: 18 October 2018 Citation: INTRODUCTION TO AUTOPHAGY Pleet ML, Branscome H, DeMarino C, Pinto DO, Zadeh MA, Rodriguez M, The discovery of the lysosome in 1955 by Christian de Duve was a landmark in the study of Sariyer IK, El-Hage N and Kashanchi F intracellular protein degradation (Ohsumi, 2014). Consequently, it was also de Duve who first used (2018) Autophagy, EVs, and Infections: A Perfect Question for a the term “autophagy,”or “self-eating” to define the phenomenon by which cytoplasmic components Perfect Time. were digested by “autolytic vacuoles or cytolysomes,” which he reasoned were lysosomes due Front. Cell. Infect. Microbiol. 8:362. to their lytic activity (de Duve et al., 1955; de Duve, 1964). While it has been over fifty years doi: 10.3389/fcimb.2018.00362 since autophagy was first described, recent decades have experienced a significant increase in Frontiers in Cellular and Infection Microbiology | www.frontiersin.org 1 October 2018 | Volume 8 | Article 362 Pleet et al. Autophagy, EVs, and Infections autophagy-related research. This interest was undoubtedly uptake and degradation. Heat shock cognate protein 70 (HSC70) spurred in the early 1990’s by Tsukada and Ohsumi’s is a major cytosolic chaperone that identifies targets that contain identification of the autophagy-related genes (ATGs) in a unique consensus motif, KFREQ, and traffics them to a yeast; an achievement for which Yoshinori Ohsumi was awarded specific lysosomal membrane receptor (LAMP2A) (Dice, 1990; the Nobel Prize in 2016 for Physiology and Medicine (Tsukada Bhattacharya and Eissa, 2015). In macroautophagy, henceforth and Ohsumi, 1993; Münz, 2017). referred to as autophagy, degradation of substrates results Autophagy is a highly conserved pathway among eukaryotes from a series of sequential steps that are carefully regulated. that involves the recognition, capture, and trafficking of various Initiation of macroautophagy occurs with the formation of intracellular components to the lysosome for degradation double-membraned structures called an autophagasomes, which (He and Klionsky, 2009; Bento et al., 2016). In the most engulfs various cytoplasmic substrates and subsequently fuses primitive sense, autophagy is responsible for maintaining with the lysosome to release its contents (Bento et al., 2016). cellular homeostasis. This is especially critical during periods of The process of autophagy is tightly controlled by a set stress and starvation; under these conditions the coordinated of ATG proteins. These proteins are further regulated by breakdown of macromolecules via autophagy machinery several mechanisms that sense energy, stress, and nutrient provides key nutrients and energy to the cell, which are required levels within the cell (White et al., 2015). Although ATGs to maintain viability (White et al., 2015; Bento et al., 2016). In were originally discovered in yeast, many of their mammalian the context of nutrient recycling, autophagy is largely considered orthologs have since been identified (Bento et al., 2016). The to be non-selective, meaning that cytoplasmic components are canonical autophagy pathway consists of a series of sequential randomly engulfed and processed for degradation. However, steps which include initiation, nucleation, elongation, and fusion advanced studies have also demonstrated that autophagy can (Bhattacharya and Eissa, 2015). Each step of this pathway is mediate the removal of specific intracellular substrates, such mediated by specific multi-protein complexes. The UNC-51-like- as misfolded proteins and damaged organelles (Gatica et al., kinase I (ULK) complex (composed of ULK1, FIP200, ATG13, 2018). This process has been termed selective autophagy and and ATG101) is responsible for the de novo formation of many different forms have been classified based on their the cup-shaped, double-membrane autophagasome during the cytosolic target. Examples of selective autophagy targets include initiation stage (Jung et al., 2009; Ktistakis and Tooze, 2016). mitochondria (mitophagy), the nucleus (nucleophagy), the The autophagasome forms at a site called the phagophore, which, endoplasmic reticulum (reticulophagy), lysosomes (lysophagy), interestingly, is a topic of active debate amongst researchers due and intracellular pathogens (xenophagy) (Ashrafi and Schwarz, to the uncertainty of the intracellular origin of this structure 2013; Hung et al., 2013; Nakatogawa and Mochida, 2015; Anding (Russell et al., 2014). In fact, the autophagosomal membranes and Baehrecke, 2017; Gatica et al., 2018). Due to the extremely are thought to arise from a wide assortment of recycled cellular diverse and specialized roles of organelles, it is imperative for membranes from the ER, mitochondria, plasma membrane, the cell to monitor and regulate their number and health. The and endosomes (Juhasz and Neufeld, 2006; Puri et al., 2013; selective removal of defective or excessive organelles protects the Bento et al., 2016; Ktistakis and Tooze, 2016). The class III cell from the buildup of toxic byproducts and, furthermore, is phosphatidylinositol-3-OH-kinase (PI(3)K) complex (composed crucial for the regulation of homeostasis. While the underlying of Beclin-1, VPS15, VPS34, and ATG14) is primarily associated mechanisms are not yet fully understood, organelle clearance with nucleation and is recruited to the growing autophagasome is believed to involve a cellular tag (i.e., ubiquitination) that by the activation of the ULK complex. PI(3)K produces marks the organelle for subsequent recognition and destruction phosphatidylinositol-3-phosphate, which subsequently recruits (Anding and Baehrecke, 2017). Thus, autophagy acts both another set of effector proteins to further drive membrane non-selectively and selectively to promote cell survival through development. Two ubiquitin-like (UBL) systems, ATG12-ATG5 nutrient recycling and to perform quality control activities and ATG8-LC3, are responsible for the elongation phase, during in the cytoplasm. Additionally, autophagy has been noted as which cytoplasmic components are engulfed by the expanding an important pathway for the processing and presentation of autophagasome (Mizushima et al., 1998; Sakoh-Nakatogawa various molecules through major histocompatibility complex et al., 2013; Bhattacharya and Eissa, 2015; Bento et al., 2016). (MHC) class proteins, especially in antigen presenting cells and The maturation and closure of the autophagosome