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Autophagy is an intracellular degradation process that delivers cytosolic material to lysosomes and vacuoles. To investigate the mechanisms that regulate autophagy, we performed a genome-wide screen using a yeast deletion-mutant collection, and found that Npr2 and Npr3 mutants were defective in autophagy. Their mammalian homologs, NPRL2 and NPRL3, were also involved in regulation of autophagy. Npr2-Npr3 function upstream of Gtr1-Gtr2, homologs of the mammalian RRAG GTPase complex, which is crucial for TORC1 regulation. Both npr2∆ mutants and a GTP-bound Gtr1 mutant suppressed autophagy and increased Tor1 vacuole localization. Furthermore, Gtr2 binds to the TORC1 subunit Kog1. A GDP-bound Gtr1 mutant induced autophagy even under nutrient-rich conditions, and this effect was dependent on the direct binding of Gtr2 to Kog1. These results revealed that 2 molecular mechanisms, Npr2-Npr3-dependent GTP hydrolysis of Gtr1 and direct binding of Gtr2 to Kog1, are involved in TORC1 inactivation and autophagic induction.

The origin and source of autophagosomal membranes are long-standing questions. By electron microscopy, we show that the endoplasmic reticulum (ER) associates with early autophagic structures called isolation membranes (IM) or phagophores in mammalian culture cells. Overexpression of a mutant of Atg4B, which causes defects in autophagosome formation, caused accumulation of ER-IM complexes. Electron tomography revealed the ER-IM complex as a subdomain of the ER forming a cradle encircling the IM, and showed that both ER and isolation membranes are interconnected.

Divergent phosphoinositides are generated to characterize specific organelles and recruit specific effector proteins to these sites. For example, phosphatidylinositol-3-phosphate (PtdIns(3)P) is a typical endosome marker and recruits many types of PtdIns(3)P binding proteins such as EEA1, Hrs, and sorting nexins, which are critical in endosomal functions. Likewise, the plasma membrane contains PtdIns(4,5)P₂, whereas the Golgi complex has PtdIns(4)P. In this sense, the endoplasmic reticulum is known to be essentially free of phosphoinositide. In other words, this situation provides the ER with the opportunity to recruit whatever proteins are in demand. Recently, we have uncovered how PtdIns(3)P is generated on the ER for the autophagic process.

Group A streptococcus (GAS) invades nonphagocytic human cells, but here it is selectively sequestered within GAS-containing autophagosome-like vacuoles (GcAVs) and killed upon fusion of GcAvs with lysosomes. GcAV formation shares core Atg machinery with canonical starvation-induced autophagy. We have recently identified a small GTPase Rab7 as a crucial factor in GcAV formation. Since Rab7 is dispensable in canonical autophagosome formation, this represents a distinction between canonical and antibacterial autophagy at the molecular level. We also showed that homotypic fusion of the initial GcAV leads to the formation of large GcAV, which is also unobserved in canonical autophagy.

Beclin 1 is an antitumor protein, required for mammalian autophagy, but its precise molecular function is poorly understood. Mass spectrometry analysis reveals that two novel proteins, Atg14L and Rubicon, associate with Beclin 1, together with a known Beclin 1-binding protein, UVRAG. The interactions of Atg14L and UVRAG with the Beclin 1-Vps34 (class III PI3-kinase)-Vps15 core complex are mutually exclusive; Rubicon associates with a subpopulation of UVRAG-containing complexes. The Atg14L complex, which positively regulates autophagy at an early step, localizes to the phagophore/isolation membrane, autophagosome and endoplasmic reticulum. In contrast, the Rubicon-UVRAG complex localizes to the late endosome/lysosome and negatively regulates both autophagy at a later step and the endocytic pathway. Thus, the Beclin 1-Vps34-Vps15 complex functions in autophagy and the endocytic pathway, but its function in a given context depends on the identity of its interacting subunits.

Recently we have reported that overexpression of an inactive mutant of Atg4B, a protease that processes pro-LC3 paralogues, inhibits lipidation of LC3 paralogues and autophagic degradation in mammalian cell. Through a mechanistic analysis, it was revealed that excess Atg4B mutant sequesters LC3 paralogues and blocks formation of Atg7-LC3 intermediate. Upon trap of LC3 paralogues, Atg5-positive autophagic structures accumulated. The structures are defective in the final closing step in autophagosome formation. The ability of the excess Atg4B mutant to inhibit autophagy provides not only an opportunity for further analysis of the LC3 system but also a useful tool available for a wide variety of experimental systems used in the study of autophagy.

Atg12 and Atg8/LC3 are two ubiquitin-like proteins involved in autophagosome formation. They show several similar characteristics just like brothers evolved from the same ancestor, however, their functional relationship has been obscure. We recently reported that a super protein complex, the Atg16L complex, which consists of multiple Atg12-Atg5 conjugates and the associating protein Atg16L, has an E3-like role in the LC3 lipidation reaction 1. The activated intermediate, LC3-Atg3 (E2) is recruited to the site where the lipidation takes place by virtue of the Atg16L complex. Thus, these two closely resembling systems are connected also in terms of their functions. This finding will provide further important clues as to the origin of the autophagosome membrane, and how the process is regulated by starvation and PtdIns3P signals.Addendum to: Fujita N, Itoh T, Fukuda M, Noda T, Yoshimori T. The Atg16L complex specifies the site of LC3 lipidation for membrane biogenesis in autophagy. Mol Biol Cell 2008:10.1091...