Mizushima, N., Levine, B., Cuervo, A.M. & Klionsky, D.J. Autophagy fights disease through cellular self-digestion. Nature451, 1069–1075 (2008). ArticleCASPubMedPubMed Central Google Scholar
Levine, B. Eating oneself and uninvited guests: autophagy-related pathways in cellular defense. Cell120, 159–162 (2005). CASPubMed Google Scholar
Kuma, A., Mizushima, N., Ishihara, N. & Ohsumi, Y. Formation of the approximately 350-kDa Apg12-Apg5.Apg16 multimeric complex, mediated by Apg16 oligomerization, is essential for autophagy in yeast. J. Biol. Chem.277, 18619–18625 (2002). ArticleCASPubMed Google Scholar
Hara, T. et al. FIP200, a ULK-interacting protein, is required for autophagosome formation in mammalian cells. J. Cell Biol.181, 497–510 (2008). ArticleCASPubMedPubMed Central Google Scholar
Sun, Q. et al. Identification of Barkor as a mammalian autophagy-specific factor for Beclin 1 and class III phosphatidylinositol 3-kinase. Proc. Natl. Acad. Sci. USA105, 19211–19216 (2008). ArticleCASPubMedPubMed Central Google Scholar
Itakura, E., Kishi, C., Inoue, K. & Mizushima, N. Beclin 1 forms two distinct phosphatidylinositol 3-kinase complexes with mammalian Atg14 and UVRAG. Mol. Biol. Cell19, 5360–5372 (2008). ArticleCASPubMedPubMed Central Google Scholar
Zhong, Y. et al. Distinct regulation of autophagic activity by Atg14L and Rubicon associated with Beclin 1–phosphatidylinositol-3-kinase complex. Nat. Cell. Biol.11, 468–476 (2009). ArticleCASPubMedPubMed Central Google Scholar
Matsunaga,K. et al. Two Beclin 1-binding proteins, Atg14L and Rubicon, reciprocally regulate autophagy at different stages. Nat. Cell Biol.11, 385–396 (2009). ArticleCASPubMed Google Scholar
Orvedahl, A. & Levine, B. Eating the enemy within: autophagy in infectious diseases. Cell Death Differ.16, 57–69 (2009). ArticleCASPubMed Google Scholar
Klionsky, D.J. et al. Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes. Autophagy4, 151–175 (2008). ArticleCASPubMed Google Scholar
Kuma, A., Matsui, M. & Mizushima, N. LC3, an autophagosome marker, can be incorporated into protein aggregates independent of autophagy: caution in the interpretation of LC3 localization. Autophagy3, 323–328 (2007). ArticleCASPubMed Google Scholar
Sanjuan, M.A. et al. Toll-like receptor signaling in macrophages links the autophagy pathway to phagocytosis. Nature450, 1253–1257 (2007). ArticleCASPubMed Google Scholar
Jackson, W.T. et al. Subversion of cellular autophagosomal machinery by RNA viruses. PLoS Biol.3, 861–871 (2005). ArticleCAS Google Scholar
Suzuki, K., Noda, T. & Ohsumi, Y. Interrelationships among Atg proteins during autophagy in Saccharomyces cerevisiae. Yeast21, 1057–1065 (2004). ArticleCASPubMed Google Scholar
Matsui, Y. et al. Distinct roles of autophagy in the heart during ischemia and reperfusion: roles of AMP-activated protein kinase and Beclin 1 in mediating autophagy. Circ. Res.100, 914–922 (2007). ArticleCASPubMed Google Scholar
Codogno, P. & Meijer, A.J. Atg5: more than an autophagy factor. Nat. Cell Biol.8, 1045–1047 (2006). ArticleCASPubMed Google Scholar
Liang, X.H. et al. Protection against fatal Sindbis virus encephalitis by beclin, a novel Bcl-2-interacting protein. J. Virol.72, 8586–8596 (1998). CASPubMedPubMed Central Google Scholar
Liu, Y. et al. Autophagy regulates programmed cell death during the plant innate immune response. Cell121, 567–577 (2005). ArticleCASPubMed Google Scholar
Orvedahl, A. et al. HSV-1 ICP34.5 Confers neurovirulence by targeting the beclin 1 autophagy protein. Cell Host Microbe1, 23–35 (2007). ArticleCASPubMed Google Scholar
Yano, T. et al. Autophagic control of listeria through intracellular innate immune recognition in Drosophila. Nat. Immunol.9, 908–916 (2008). ArticleCASPubMedPubMed Central Google Scholar
Kim, P.K., Hailey, D.W., Mullen, R.T. & Lippincott-Schwartz, J. Ubiquitin signals autophagic degradation of cytosolic proteins and peroxisomes. Proc. Natl. Acad. Sci. USA105, 20567–20574 (2008). ArticleCASPubMedPubMed Central Google Scholar
Zhao, Z. et al. Autophagosome-independent essential function for the autophagy protein Atg5 in cellular immunity to intracellular pathogens. Cell Host Microbe4, 458–469 (2008). ArticleCASPubMedPubMed Central Google Scholar
Martens, S. et al. Disruption of Toxoplasma gondii parasitophorous vacuoles by the mouse p47-resistance GTPases. PLoS Pathog.1, e24 (2005). ArticlePubMedPubMed Central Google Scholar
Ling, Y.M. et al. Vacuolar and plasma membrane stripping and autophagic elimination of Toxoplasma gondii in primed effector macrophages. J. Exp. Med.203, 2063–2071 (2006). ArticleCASPubMedPubMed Central Google Scholar
Zhao, Y.O., Khaminets, A., Hunn, J.P. & Howard, J.C. Disruption of the Toxoplasma gondii parasitophorous vacuole by IFNγ−inducible immunity-related GTPases (IRG proteins) triggers necrotic cell death. PLoS Pathog.5, e1000288 (2009). ArticlePubMedPubMed Central Google Scholar
Gutierrez, M.G. et al. Autophagy is a defense mechanism inhibiting BCG and Mycobacterium tuberculosis survival in infected macrophages. Cell119, 753–766 (2004). ArticleCASPubMed Google Scholar
Singh, S.B., Davis, A.S., Taylor, G.A. & Deretic, V. Human IRGM induces autophagy to eliminate intracellular mycobacteria. Science313, 1438–1441 (2006). ArticleCASPubMed Google Scholar
Harris, J. et al. T helper 2 cytokines inhibit autophagic control of intracellular Mycobacterium tuberculosis. Immunity27, 505–517 (2007). ArticleCASPubMed Google Scholar
Taylor, G.A., Feng, C.G. & Sher, A. p47 GTPases: regulators of immunity to intracellular pathogens. Nat. Rev. Immunol.4, 100–109 (2004). ArticleCASPubMed Google Scholar
Papic, N., Hunn, J.P., Pawlowski, N., Zerrahn, J. & Howard, J.C. Inactive and active states of the interferon-inducible resistance GTPase, Irga6, in vivo. J. Biol. Chem.283, 32143–32151 (2008). ArticleCASPubMedPubMed Central Google Scholar
Feng, C.G. et al. The immunity-related GTPase Irgm1 promotes the expansion of activated CD4+ T cell populations by preventing interferon-γ-induced cell death. Nat. Immunol.9, 1279–1287 (2008). ArticleCASPubMedPubMed Central Google Scholar
Delgado, M.A., Elmaoued, R.A., Davis, A.S., Kyei, G. & Deretic, V. Toll-like receptors control autophagy. EMBO J.27, 1110–1121 (2008). ArticleCASPubMedPubMed Central Google Scholar
Lee, H.K., Lund, J.M., Ramanathan, B., Mizushima, N. & Iwasaki, A. Autophagy-dependent viral recognition by plasmacytoid dendritic cells. Science315, 1398–1401 (2007). ArticleCASPubMed Google Scholar
Saitoh, T. et al. Loss of the autophagy protein Atg16L1 enhances endotoxin-induced IL-1β production. Nature456, 264–268 (2008). ArticleCASPubMed Google Scholar
Shui, W. et al. Membrane proteomics of phagosomes suggests a connection to autophagy. Proc. Natl. Acad. Sci. USA105, 16952–16957 (2008). ArticleCASPubMedPubMed Central Google Scholar
Jounai, N. et al. The Atg5 Atg12 conjugate associates with innate antiviral immune responses. Proc. Natl. Acad. Sci. USA104, 14050–14055 (2007). ArticleCASPubMedPubMed Central Google Scholar
Tal, M.C. et al. Absence of autophagy results in reactive oxygen species-dependent amplification of RLR signaling. Proc. Natl. Acad. Sci. USA106, 2770–2775 (2009). ArticleCASPubMedPubMed Central Google Scholar
Cadwell, K. et al. A key role for autophagy and the autophagy gene Atg16l1 in mouse and human intestinal Paneth cells. Nature456, 259–263 (2008). ArticleCASPubMedPubMed Central Google Scholar
Petrilli, V., Dostert, C., Muruve, D.A. & Tschopp, J. The inflammasome: a danger sensing complex triggering innate immunity. Curr. Opin. Immunol.19, 615–622 (2007). ArticleCASPubMed Google Scholar
Kanneganti, T.D., Lamkanfi, M. & Nunez, G. Intracellular NOD-like receptors in host defense and disease. Immunity27, 549–559 (2007). ArticleCASPubMed Google Scholar
Lunemann, J.D. & Munz, C. Autophagy in CD4+ T-cell immunity and tolerance. Cell Death Differ.16, 79–86 (2009). ArticleCASPubMed Google Scholar
English, D. et al. Autophagy enhances the presentation of endogenous viral antigens on MHC class I molecules during HSV-1 infection. Nat. Immunol.10, 480–487 (2009). ArticleCASPubMed Google Scholar
Paludan, C. et al. Endogenous MHC class II processing of a viral nuclear antigen after autophagy. Science307, 593–596 (2005). ArticleCASPubMed Google Scholar
Schmid, D., Pypaert, M. & Munz, C. Antigen-loading compartments for major histocompatibility complex class II molecules continuously receive input from autophagosomes. Immunity26, 79–92 (2007). ArticleCASPubMed Google Scholar
Mizushima, N., Yamamoto, A., Matsui, M., Yoshimori, T. & Ohsumi, Y. In vivo analysis of autophagy in response to nutrient starvation using transgenic mice expressing a fluorescent autophagosome marker. Mol. Biol. Cell15, 1101–1111 (2004). ArticleCASPubMedPubMed Central Google Scholar
Nedjic, J., Aichinger, M., Emmerich, J., Mizushima, N. & Klein, L. Autophagy in thymic epithelium shapes the T-cell repertoire and is essential for tolerance. Nature455, 396–400 (2008). ArticleCASPubMed Google Scholar
Qu, X. et al. Autophagy gene-dependent clearance of apoptotic cells during embryonic development. Cell128, 931–946 (2007). ArticleCASPubMed Google Scholar
Mellen, M.A., de la Rosa, E.J. & Boya, P. The autophagic machinery is necessary for removal of cell corpses from the developing retinal neuroepithelium. Cell Death Differ.15, 1279–1290 (2008). ArticleCASPubMed Google Scholar
Arsov, I. et al. BAC-mediated transgenic expression of fluorescent autophagic protein Beclin 1 reveals a role for Beclin 1 in lymphocyte development. Cell Death Differ.15, 1385–1395 (2008). ArticleCASPubMed Google Scholar
Stephenson, L.M. et al. Identification of _Atg5_-dependent transcriptional changes and increases in mitochondrial mass in _Atg5_-deficient T lymphocytes. Autophagy (in the press).
Pua, H.H., Dzhagalov, I., Chuck, M., Mizushima, N. & He, Y.W. A critical role for the autophagy gene Atg5 in T cell survival and proliferation. J. Exp. Med.204, 25–31 (2007). ArticleCASPubMedPubMed Central Google Scholar
Pua, H.H., Guo, J., Komatsu, M. & He, Y.W. Autophagy is essential for mitochondrial clearance in mature T lymphocytes. J. Immunol.182, 4046–4055 (2009). ArticleCASPubMed Google Scholar
Miller, B.C. et al. The autophagy gene ATG5 plays an essential role in B lymphocyte development. Autophagy4, 309–314 (2007). ArticlePubMed Google Scholar
Li, C. et al. Autophagy is induced in CD4+ T cells and important for the growth factor-withdrawal cell death. J. Immunol.177, 5163–5168 (2006). ArticleCASPubMed Google Scholar
Espert, L. et al. Autophagy is involved in T cell death after binding of HIV-1 envelope proteins to CXCR4. J. Clin. Invest.116, 2161–2172 (2006). ArticleCASPubMedPubMed Central Google Scholar
Bell, B.D. et al. FADD and caspase-8 control the outcome of autophagic signaling in proliferating T cells. Proc. Natl. Acad. Sci. USA105, 16677–16682 (2008). ArticleCASPubMedPubMed Central Google Scholar
Arbour, N. et al. c-Jun NH2-terminal kinase (JNK)1 and JNK2 signaling pathways have divergent roles in CD8+ T cell-mediated antiviral immunity. J. Exp. Med.195, 801–810 (2002). ArticleCASPubMedPubMed Central Google Scholar
Conze, D. et al. c-Jun NH2-terminal kinase (JNK)1 and JNK2 have distinct roles in CD8+ T cell activation. J. Exp. Med.195, 811–823 (2002). ArticleCASPubMedPubMed Central Google Scholar
Dong, C. et al. Defective T cell differentiation in the absence of Jnk1. Science282, 2092–2095 (1998). ArticleCASPubMed Google Scholar
Wei, Y., Pattingre, S., Sinha, S., Bassik, M. & Levine, B. JNK1-mediated phosphorylation of Bcl-2 regulates starvation-induced autophagy. Mol. Cell30, 678–688 (2008). ArticleCASPubMedPubMed Central Google Scholar
Barrett, J.C. et al. Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease. Nat. Genet.40, 955–962 (2008). ArticleCASPubMedPubMed Central Google Scholar
Massey, D.C. & Parkes, M. Genome-wide association scanning highlights two autophagy genes, ATG16L1 and IRGM, as being significantly associated with Crohn's disease. Autophagy3, 649–651 (2007). ArticleCASPubMed Google Scholar
The Wellcome Trust Case Control Consortium. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature447, 661–678 (2007).
McCarroll, S.A. et al. Deletion polymorphism upstream of IRGM associated with altered IRGM expression and Crohn's disease. Nat. Genet.40, 1107–1112 (2008). ArticleCASPubMedPubMed Central Google Scholar
Rioux, J.D. et al. Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesis. Nat. Genet.39, 596–604 (2007). ArticleCASPubMedPubMed Central Google Scholar
Kuballa, P., Huett, A., Rioux, J.D., Daly, M.J. & Xavier, R.J. Impaired autophagy of an intracellular pathogen induced by a Crohn's disease associated ATG16L1 variant. PLoS ONE3, e3391 (2008). ArticlePubMedPubMed Central Google Scholar
Vaishnava, S., Behrendt, C.L., Ismail, A.S., Eckmann, L. & Hooper, L.V. Paneth cells directly sense gut commensals and maintain homeostasis at the intestinal host-microbial interface. Proc. Natl. Acad. Sci. USA105, 20858–20863 (2008). ArticleCASPubMedPubMed Central Google Scholar
Kaser, A. et al. XBP1 links ER stress to intestinal inflammation and confers genetic risk for human inflammatory bowel disease. Cell134, 743–756 (2008). ArticleCASPubMedPubMed Central Google Scholar
Cadwell, K., Patel, K.K., Komatsu, M., Virgin, H.W. & Stappenbeck, T.S. A common role for Atg16L1, Atg5, and Atg7 in small intestinal Paneth cells and Crohn's disease. Autophagy5, 250–252 (2008). Article Google Scholar