Viruses have played an important role in human evolution and have evolved diverse strategies to co-exist with their hosts. As obligate intracellular pathogens, viruses exploit and manipulate different host cell processes, including cellular trafficking, metabolism and immunity-related functions, for their own survival. In this article, we review evidence for how autophagy, a highly conserved cellular degradative pathway, serves either as an antiviral defense mechanism or, alternatively, as a pro-viral process during virus infection. Furthermore, we highlight recent reports concerning the role of selective autophagy in virus infection and how viruses manipulate autophagy to evade lysosomal capture and degradation.
Mijaljica, D.; Prescott, M.; Devenish, R.J. Microautophagy in mammalian cells: Revisiting a 40-year-old conundrum. Autophagy 2011, 7, 673–682, doi:10.4161/auto.7.7.14733.
[3]
Dunn, W.A., Jr. Studies on the mechanisms of autophagy: Formation of the autophagic vacuole. J. Cell Biol. 1990, 110, 1923–1933, doi:10.1083/jcb.110.6.1923.
[4]
Fengsrud, M.; Erichsen, E.S.; Berg, T.O.; Raiborg, C.; Seglen, P.O. Ultrastructural characterization of the delimiting membranes of isolated autophagosomes and amphisomes by freeze-fracture electron microscopy. Eur. J. Cell Biol. 2000, 79, 871–882, doi:10.1078/0171-9335-00125.
[5]
Eskelinen, E.L. Maturation of autophagic vacuoles in Mammalian cells. Autophagy 2005, 1, 1–10, doi:10.4161/auto.1.1.1270.
[6]
Axe, E.L.; Walker, S.A.; Manifava, M.; Chandra, P.; Roderick, H.L.; Habermann, A.; Griffiths, G.; Ktistakis, N.T. Autophagosome formation from membrane compartments enriched in phosphatidylinositol 3-phosphate and dynamically connected to the endoplasmic reticulum. J. Cell Biol. 2008, 182, 685–701, doi:10.1083/jcb.200803137.
[7]
Hailey, D.W.; Rambold, A.S.; Satpute-Krishnan, P.; Mitra, K.; Sougrat, R.; Kim, P.K.; Lippincott-Schwartz, J. Mitochondria supply membranes for autophagosome biogenesis during starvation. Cell 2010, 141, 656–667, doi:10.1016/j.cell.2010.04.009.
[8]
Ravikumar, B.; Moreau, K.; Jahreiss, L.; Puri, C.; Rubinsztein, D.C. Plasma membrane contributes to the formation of pre-autophagosomal structures. Nature Cell Biol. 2010, 12, 747–757, doi:10.1038/ncb2078.
[9]
Inoue, Y.; Klionsky, D.J. Regulation of macroautophagy in Saccharomyces cerevisiae. Semin. Cell Dev. Biol. 2010, 21, 664–670, doi:10.1016/j.semcdb.2010.03.009.
[10]
Kirkin, V.; McEwan, D.G.; Novak, I.; Dikic, I. A role for ubiquitin in selective autophagy. Mol. Cell 2009, 34, 259–269, doi:10.1016/j.molcel.2009.04.026.
[11]
Behrends, C.; Fulda, S. Receptor proteins in selective autophagy. Int. J. Cell Biol. 2012, 2012, 673290.
[12]
Novak, I.; Dikic, I. Autophagy receptors in developmental clearance of mitochondria. Autophagy 2011, 7, 301–303, doi:10.4161/auto.7.3.14509.
[13]
Deribe, Y.L.; Pawson, T.; Dikic, I. Post-translational modifications in signal integration. Nat. Struct. Mol. Biol. 2010, 17, 666–672.
[14]
McEwan, D.G.; Dikic, I. The Three Musketeers of Autophagy: phosphorylation, ubiquitylation and acetylation. Trends Cell Biol. 2011, 21, 195–201, doi:10.1016/j.tcb.2010.12.006.
[15]
Behrends, C.; Sowa, M.E.; Gygi, S.P.; Harper, J.W. Network organization of the human autophagy system. Nature 2010, 466, 68–76.
Dreux, M.; Gastaminza, P.; Wieland, S.F.; Chisari, F.V. The autophagy machinery is required to initiate hepatitis C virus replication. PNAS 2009, 106, 14046–14051.
[27]
Gannage, M.; Dormann, D.; Albrecht, R.; Dengjel, J.; Torossi, T.; Ramer, P.C.; Lee, M.; Strowig, T.; Arrey, F.; Conenello, G.; Pypaert, M.; Andersen, J.; Garcia-Sastre, A.; Munz, C. Matrix protein 2 of influenza A virus blocks autophagosome fusion with lysosomes. Cell Host Microbe 2009, 6, 367–380, doi:10.1016/j.chom.2009.09.005.
[28]
Kyei, G.B.; Dinkins, C.; Davis, A.S.; Roberts, E.; Singh, S.B.; Dong, C.; Wu, L.; Kominami, E.; Ueno, T.; Yamamoto, A.; Federico, M.; Panganiban, A.; Vergne, I.; Deretic, V. Autophagy pathway intersects with HIV-1 biosynthesis and regulates viral yields in macrophages. J. Cell Biol. 2009, 186, 255–268, doi:10.1083/jcb.200903070.
[29]
Panyasrivanit, M.; Khakpoor, A.; Wikan, N.; Smith, D.R. Linking dengue virus entry and translation/replication through amphisomes. Autophagy 2009, 5, 434–435, doi:10.4161/auto.5.3.7925.
[30]
Panyasrivanit, M.; Khakpoor, A.; Wikan, N.; Smith, D.R. Co-localization of constituents of the dengue virus translation and replication machinery with amphisomes. J. Gen. Virol. 2009, 90, 448–456, doi:10.1099/vir.0.005355-0.
[31]
Shelly, S.; Lukinova, N.; Bambina, S.; Berman, A.; Cherry, S. Autophagy is an essential component of Drosophila immunity against vesicular stomatitis virus. Immunity 2009, 30, 588–598, doi:10.1016/j.immuni.2009.02.009.
[32]
Takahashi, M.N.; Jackson, W.; Laird, D.T.; Culp, T.D.; Grose, C.; Haynes, J.I., 2nd; Benetti, L. Varicella-zoster virus infection induces autophagy in both cultured cells and human skin vesicles. JVI 2009, 83, 5466–5476, doi:10.1128/JVI.02670-08.
[33]
Tang, H.; Da, L.; Mao, Y.; Li, Y.; Li, D.; Xu, Z.; Li, F.; Wang, Y.; Tiollais, P.; Li, T.; Zhao, M. Hepatitis B virus X protein sensitizes cells to starvation-induced autophagy via up-regulation of beclin 1 expression. Hepatology 2009, 49, 60–71, doi:10.1002/hep.22581.
[34]
Zhou, Z.; Jiang, X.; Liu, D.; Fan, Z.; Hu, X.; Yan, J.; Wang, M.; Gao, G.F. Autophagy is involved in influenza A virus replication. Autophagy 2009, 5, 321–328, doi:10.4161/auto.5.3.7406.
[35]
Khakpoor, A.; Panyasrivanit, M.; Wikan, N.; Smith, D.R. A role for autophagolysosomes in dengue virus 3 production in HepG2 cells. J. Gen. Virol. 2009, 90, 1093–1103, doi:10.1099/vir.0.007914-0.
[36]
Ke, P.Y.; Chen, S.S. Activation of the unfolded protein response and autophagy after hepatitis C virus infection suppresses innate antiviral immunity in vitro. J. Clin. Invest. 2011, 121, 37–56, doi:10.1172/JCI41474.
[37]
Orvedahl, A.; MacPherson, S.; Sumpter, R., Jr.; Talloczy, Z.; Zou, Z.; Levine, B. Autophagy protects against Sindbis virus infection of the central nervous system. Cell Host Microbe 2010, 7, 115–127, doi:10.1016/j.chom.2010.01.007.
[38]
Liang, C.; E, X.; Jung, J.U. Downregulation of autophagy by herpesvirus Bcl-2 homologs. Autophagy 2008, 4, 268–272.
[39]
Ku, B.; Woo, J.S.; Liang, C.; Lee, K.H.; Hong, H.S.; E, X.; Kim, K.S.; Jung, J.U.; Oh, B.H. Structural and biochemical bases for the inhibition of autophagy and apoptosis by viral BCL-2 of murine gamma-herpesvirus 68. PLoS Pathog. 2008, 4, e25, doi:10.1371/journal.ppat.0040025.
Levine, B.; Deretic, V. Unveiling the roles of autophagy in innate and adaptive immunity. Nat. Rev. Immunol. 2007, 7, 767–777, doi:10.1038/nri2161.
[42]
Kemball, C.C.; Alirezaei, M.; Flynn, C.T.; Wood, M.R.; Harkins, S.; Kiosses, W.B.; Whitton, J.L. Coxsackievirus infection induces autophagy-like vesicles and megaphagosomes in pancreatic acinar cells in vivo. JVI 2010, 84, 12110–12124, doi:10.1128/JVI.01417-10.
[43]
Joubert, P.E.; Meiffren, G.; Gregoire, I.P.; Pontini, G.; Richetta, C.; Flacher, M.; Azocar, O.; Vidalain, P.O.; Vidal, M.; Lotteau, V.; Codogno, P.; Rabourdin-Combe, C.; Faure, M. Autophagy induction by the pathogen receptor CD46. Cell Host Microbe 2009, 6, 354–366, doi:10.1016/j.chom.2009.09.006.
[44]
Denizot, M.; Varbanov, M.; Espert, L.; Robert-Hebmann, V.; Sagnier, S.; Garcia, E.; Curriu, M.; Mamoun, R.; Blanco, J.; Biard-Piechaczyk, M. HIV-1 gp41 fusogenic function triggers autophagy in uninfected cells. Autophagy 2008, 4, 998–1008.
[45]
Espert, L.; Denizot, M.; Grimaldi, M.; Robert-Hebmann, V.; Gay, B.; Varbanov, M.; Codogno, P.; Biard-Piechaczyk, M. Autophagy is involved in T cell death after binding of HIV-1 envelope proteins to CXCR4. J. Clin. Invest. 2006, 116, 2161–2172, doi:10.1172/JCI26185.
[46]
Nakamoto, M.; Moy, R.H.; Xu, J.; Bambina, S.; Yasunaga, A.; Shelly, S.S.; Gold, B.; Cherry, S. Virus recognition by Toll-7 activates antiviral autophagy in Drosophila. Immunity 2012, 36, 658–667, doi:10.1016/j.immuni.2012.03.003.
[47]
Kroemer, G.; Marino, G.; Levine, B. Autophagy and the integrated stress response. Mol. Cell 2010, 40, 280–293, doi:10.1016/j.molcel.2010.09.023.
[48]
Martinon, F. The endoplasmic reticulum: A sensor of cellular stress that modulates immune responses. Microbes Infect. 2012, 14, 1293–1300, doi:10.1016/j.micinf.2012.07.005.
[49]
Mohl, B.P.; Tedbury, P.R.; Griffin, S.; Harris, M. Hepatitis C virus-induced autophagy is independent of the unfolded protein response. JVI 2012, 86, 10724–10732, doi:10.1128/JVI.01667-12.
[50]
McLean, J.E.; Wudzinska, A.; Datan, E.; Quaglino, D.; Zakeri, Z. Flavivirus NS4A-induced autophagy protects cells against death and enhances virus replication. J. Biol. Chem. 2011, 286, 22147–22159.
[51]
Carpenter, J.E.; Jackson, W.; Benetti, L.; Grose, C. Autophagosome formation during varicella-zoster virus infection following endoplasmic reticulum stress and the unfolded protein response. JVI 2011, 85, 9414–9424, doi:10.1128/JVI.00281-11.
Ramos, H.J.; Gale, M., Jr. RIG-I like receptors and their signaling crosstalk in the regulation of antiviral immunity. Curr. Opin. Virol. 2011, 1, 167–176, doi:10.1016/j.coviro.2011.04.004.
Munz, C. Antigen processing by macroautophagy for MHC presentation. FIMMU 2011, 2, 42.
[64]
Martinez-Borra, J.; Lopez-Larrea, C. The emergence of the major histocompatilibility complex. Adv. Exp. Med. Biol. 2012, 738, 277–289, doi:10.1007/978-1-4614-1680-7_16.
[65]
Joffre, O.P.; Segura, E.; Savina, A.; Amigorena, S. Cross-presentation by dendritic cells. Nat. Rev. Immunol. 2012, 12, 557–569.
[66]
Gannage, M.; Munz, C. MHC presentation via autophagy and how viruses escape from it. Semin. Immunopathol. 2010, 32, 373–381, doi:10.1007/s00281-010-0227-7.
[67]
English, L.; Chemali, M.; Duron, J.; Rondeau, C.; Laplante, A.; Gingras, D.; Alexander, D.; Leib, D.; Norbury, C.; Lippe, R.; Desjardins, M. Autophagy enhances the presentation of endogenous viral antigens on MHC class I molecules during HSV-1 infection. Nat. Immunol. 2009, 10, 480–487, doi:10.1038/ni.1720.
[68]
Leung, C.S.; Taylor, G.S. Nuclear shelter: The influence of subcellular location on the processing of antigens by macroautophagy. Autophagy 2010, 6.
[69]
Paludan, C.; Schmid, D.; Landthaler, M.; Vockerodt, M.; Kube, D.; Tuschl, T.; Munz, C. Endogenous MHC class II processing of a viral nuclear antigen after autophagy. Science 2005, 307, 593–596.
[70]
Schmid, D.; Pypaert, M.; Munz, C. Antigen-loading compartments for major histocompatibility complex class II molecules continuously receive input from autophagosomes. Immunity 2007, 26, 79–92, doi:10.1016/j.immuni.2006.10.018.
[71]
Miller, S.; Krijnse-Locker, J. Modification of intracellular membrane structures for virus replication. Nat. Rev. Microbiol. 2008, 6, 363–374, doi:10.1038/nrmicro1890.
[72]
Schlegel, A.; Giddings, T.H., Jr.; Ladinsky, M.S.; Kirkegaard, K. Cellular origin and ultrastructure of membranes induced during poliovirus infection. JVI 1996, 70, 6576–6588.
[73]
Huang, S.C.; Chang, C.L.; Wang, P.S.; Tsai, Y.; Liu, H.S. Enterovirus 71-induced autophagy detected in vitro and in vivo promotes viral replication. J. Med. Virol. 2009, 81, 1241–1252.
[74]
O'Donnell, V.; Pacheco, J.M.; LaRocco, M.; Burrage, T.; Jackson, W.; Rodriguez, L.L.; Borca, M.V.; Baxt, B. Foot-and-mouth disease virus utilizes an autophagic pathway during viral replication. Virology 2011, 410, 142–150, doi:10.1016/j.virol.2010.10.042.
[75]
Belov, G.A.; Altan-Bonnet, N.; Kovtunovych, G.; Jackson, C.L.; Lippincott-Schwartz, J.; Ehrenfeld, E. Hijacking components of the cellular secretory pathway for replication of poliovirus RNA. JVI 2007, 81, 558–567, doi:10.1128/JVI.01820-06.
[76]
Belov, G.A.; Feng, Q.; Nikovics, K.; Jackson, C.L.; Ehrenfeld, E. A critical role of a cellular membrane traffic protein in poliovirus RNA replication. PLoS Pathog. 2008, 4, e1000216.
[77]
Hsu, N.Y.; Ilnytska, O.; Belov, G.; Santiana, M.; Chen, Y.H.; Takvorian, P.M.; Pau, C.; van der Schaar, H.; Kaushik-Basu, N.; Balla, T.; Cameron, C.E.; Ehrenfeld, E.; van Kuppeveld, F.J.; Altan-Bonnet, N. Viral reorganization of the secretory pathway generates distinct organelles for RNA replication. Cell 2010, 141, 799–811, doi:10.1016/j.cell.2010.03.050.
[78]
Taylor, M.P.; Burgon, T.B.; Kirkegaard, K.; Jackson, W.T. Role of microtubules in extracellular release of poliovirus. JVI 2009, 83, 6599–6609, doi:10.1128/JVI.01819-08.
[79]
Sir, D.; Kuo, C.F.; Tian, Y.; Liu, H.M.; Huang, E.J.; Jung, J.U.; Machida, K.; Ou, J.H. Replication of hepatitis C virus RNA on autophagosomal membranes. J. Biol. Chem. 2012, 287, 18036–18043.
[80]
Tanida, I.; Fukasawa, M.; Ueno, T.; Kominami, E.; Wakita, T.; Hanada, K. Knockdown of autophagy-related gene decreases the production of infectious hepatitis C virus particles. Autophagy 2009, 5, 937–945, doi:10.4161/auto.5.7.9243.
[81]
Taguwa, S.; Kambara, H.; Fujita, N.; Noda, T.; Yoshimori, T.; Koike, K.; Moriishi, K.; Matsuura, Y. Dysfunction of autophagy participates in vacuole formation and cell death in cells replicating hepatitis C virus. JVI 2011, 85, 13185–13194, doi:10.1128/JVI.06099-11.
[82]
Shrivastava, S.; Raychoudhuri, A.; Steele, R.; Ray, R.; Ray, R.B. Knockdown of autophagy enhances the innate immune response in hepatitis C virus-infected hepatocytes. Hepatology 2011, 53, 406–414, doi:10.1002/hep.24073.
Knoops, K.; Kikkert, M.; Worm, S.H.; Zevenhoven-Dobbe, J.C.; van der Meer, Y.; Koster, A.J.; Mommaas, A.M.; Snijder, E.J. SARS-coronavirus replication is supported by a reticulovesicular network of modified endoplasmic reticulum. PLoS Biol. 2008, 6, e226, doi:10.1371/journal.pbio.0060226.
[86]
Reggiori, F.; Monastyrska, I.; Verheije, M.H.; Cali, T.; Ulasli, M.; Bianchi, S.; Bernasconi, R.; de Haan, C.A.; Molinari, M. Coronaviruses Hijack the LC3-I-positive EDEMosomes, ER-derived vesicles exporting short-lived ERAD regulators, for replication. Cell Host Microbe 2010, 7, 500–508, doi:10.1016/j.chom.2010.05.013.
[87]
Heaton, N.S.; Randall, G. Dengue virus and autophagy. Viruses 2011, 3, 1332–1341, doi:10.3390/v3081332.
[88]
Li, J.; Liu, Y.; Wang, Z.; Liu, K.; Wang, Y.; Liu, J.; Ding, H.; Yuan, Z. Subversion of cellular autophagy machinery by hepatitis B virus for viral envelopment. JVI 2011, 85, 6319–6333, doi:10.1128/JVI.02627-10.
[89]
Deretic, V.; Jiang, S.; Dupont, N. Autophagy intersections with conventional and unconventional secretion in tissue development, remodeling and inflammation. Trends Cell Biol. , 2012.
[90]
Fliss, P.M.; Jowers, T.P.; Brinkmann, M.M.; Holstermann, B.; Mack, C.; Dickinson, P.; Hohenberg, H.; Ghazal, P.; Brune, W. Viral mediated redirection of NEMO/IKKgamma to autophagosomes curtails the inflammatory cascade. PLoS Pathog. 2012, 8, e1002517.
[91]
Gregoire, I.P.; Richetta, C.; Meyniel-Schicklin, L.; Borel, S.; Pradezynski, F.; Diaz, O.; Deloire, A.; Azocar, O.; Baguet, J.; Le Breton, M.; Mangeot, P.E.; Navratil, V.; Joubert, P.E.; Flacher, M.; Vidalain, P.O.; Andre, P.; Lotteau, V.; Biard-Piechaczyk, M.; Rabourdin-Combe, C.; Faure, M. IRGM is a common target of RNA viruses that subvert the autophagy network. PLoS Pathog. 2011, 7, e1002422.