[Abstract unavailable

The substrates of mammalian ULK1/2 and its yeast homologue Atg1 in autophagy have remained elusive. The class III phosphatidylinositol 3-kinase component Beclin-1 has now been identified as a physiological substrate of the ULK kinases in autophagy following amino acid starvation, therefore suggesting a critical molecular link between the upstream kinases and the autophagy core machinery.Autophagy is a specialized degradative route, which starts with the formation of autophagosomes and ends in the lysosomes, providing building blocks and energy for cellular survival 1 . More than 36 autophagy-related genes (Atgs) have been identified in yeast, and most of them are evolutionarily conserved 2 . Among these Atg proteins, there is only one serine/threonine protein kinase: Atg1 in yeast and ULK1/2 in mammals 3 . The kinase activity of ULK/Atg1 is required for autophagy, but its physiological substrates have, until recently, been unknown. In this issue, Guan and colleagues demonstrate that ULK phosphorylates Beclin-1 following amino acid withdrawal, and this phosphorylation step is crucial for the function of Beclin-1 in autophagy 4 .Beclin-1, the mammalian homologue of yeast Atg6, serves as a core component of the class III phosphatidylinositol 3-kinase (PI(3)KC3) complex. The PI(3)KC3 complex is composed of at least six stoichiometric subunits, including VPS34 (the mammalian counterpart of yeast Vps34), p150 (counterpart of yeast Vps15), Beclin-1 (Atg6 in yeast), ATG14L (also known as Barkor; Atg14 in yeast), UVRAG (Vps38 in yeast) and Rubicon (which has no yeast counterpart) [5][6][7][8][9][10] . VPS34, p150 and Beclin-1 form a stable core complex, and Beclin-1 is proposed to function as a bridge between the core complex and the regulatory subunits such as ATG14L or UVRAG. Activity of PI(3)KC3 is essential for autophagy initiation, and therefore it is tightly regulated. Guan and colleagues have developed an elegant in vitro assay for VPS34 activity, in which endogenous VPS34 is immunopurified from mammalian cell lysates that have been subjected to various environmental stresses, including glucose starvation and amino acid shortage 4,11 . They found that VPS34 lipid kinase activity is different depending on which subunit is associated with the VPS34 complex. Following

Ypt/Rab GTPases are key regulators of all membrane trafficking events in eukaryotic cells. They act as molecular switches that attach to membranes via lipid tails to recruit their multiple downstream effectors, which mediate vesicular transport. Originally discovered in yeast as Ypts, they were later shown to be conserved from yeast to humans, where Rabs are relevant to a wide array of diseases. Major principles learned from our past studies in yeast are currently accepted in the Ypt/Rab field including: i) Ypt/Rabs are not transport-step specific, but are rather compartment specific, ii) stimulation by nucleotide exchangers, GEFs, is critical to their function, whereas GTP hydrolysis plays a role in their cycling between membranes and the cytoplasm for multiple rounds of action, iii) they mediate diverse functions ranging from vesicle formation to vesicle fusion, and iv) they act in GTPase cascades to regulate intracellular trafficking pathways. Our recent studies on Ypt1 and Ypt31/Ypt32 and their modular GEF complex TRAPP raise three exciting novel paradigms for Ypt/Rab function: (a) coordination of vesicular transport substeps, (b) integration of individual transport steps into pathways, and (c) coordination of different transport pathways. In addition to its amenability to genetic analysis, yeast provides a superior model system for future studies on the role of Ypt/Rabs in traffic coordination due to the smaller proteome that results in a simpler traffic grid. We propose that different types of coordination are important also in human cells for fine-tuning of intracellular trafficking, and that coordination defects could result in disease.

In methylotrophic yeasts, peroxisomes are required for methanol utilization, but are dispensable for growth on most other carbon sources. Upon adaptation of cells grown on methanol to glucose or ethanol, redundant peroxisomes are selectively and quickly shipped to, and degraded in, vacuoles via a process termed pexophagy. We identified a novel gene named ATG28 (autophagy-related genes) involved in pexophagy in the yeast Pichia pastoris. This yeast exhibits two morphologically distinct pexophagy pathways, micro- and macropexophagy, induced by glucose or ethanol, respectively. Deficiency in ATG28 impairs both pexophagic mechanisms but not general (bulk turnover) autophagy, a degradation pathway in yeast triggered by nitrogen starvation. It is known that the micro-, macropexophagy, and general autophagy machineries are distinct but share some molecular components. The identification of ATG28 suggests that pexophagy may involve species-specific components, since this gene appears to have only weak homologues in other yeasts.

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