Edited by Thomas Sö llnerThe small GTP-binding protein Rab12 plays an important role in the initiation of starvation-induced macroautophagy (autophagy) and is activated by the guanine-nucleotide exchange factor DENND3. However, the molecular mechanism by which DENND3 becomes activated has remained elusive. Xu and McPherson now identify a novel mechanism of DENND3 intramolecular binding that is regulated by the phosphorylation of a single tyrosine residue.Autophagy is a means of selectively marking cellular organelles for lysosomal degradation and plays a vital role in the recycling of proteins during stress caused by nutrient deprivation (1). During this process, various protein complexes (known as initiation and nucleation complexes) first localize to a membrane-phagophore assembly site and then recruit additional autophagy-related proteins to elongate the phagophore membrane. Eventually, the phagophore closes into an autophagosome, which ultimately fuses with the lysosome. Despite the considerable advances that have been made in understanding the molecular processes of autophagosome formation and its fusion with lysosomes, the mechanisms by which nutrient deprivation induces the initiation of this process remains poorly understood.The Rab family of small GTP-binding proteins plays an essential role in membrane-trafficking pathways, including the control of various steps of autophagy. In particular, Rab12 has been identified recently as a key player in autophagy, and its depletion severely impairs the autophagic process (2, 3). To function in autophagy, Rab12 needs to become GTP-loaded and activated, and the DENN (differentially expressed in normal and neoplastic cells) protein DENND3 was identified as its guanine nucleotide exchange factor (GEF) 2 (4). As the DENN domain-containing proteins comprise the largest family of Rab-GTP exchange factors, understanding their mechanisms of action has ramifications beyond DENND3 and Rab12. To date, the molecular mechanisms of DENND3 activation and its induction by nutrient deprivation are not well understood. It is known that serum starvation leads to the activation of a kinase known as Unc-51-like kinase (ULK), which subsequently phosphorylates serines 554 and 572 on DENND3 (5). This, in turn, allows recruitment of the adapter protein, 14-3-3, to DENND3, which somehow leads to up-regulation of DENND3 GEF activity toward Rab12. However, whether there is a separate mechanism to more precisely regulate DENND3 in response to serum starvation remains a central and unanswered question.In this exciting paper by Xu and McPherson (6), the authors shed new light on the mechanism by which the Rab12 GEF, DENND3, becomes activated upon serum starvation. Because the "linker" region of DENND3 (which extends from amino acids 520 -973) contains both serines 554 and 572 that are phosphorylated by ULK, the authors initially hypothesized that the linker region might interact with the DENN domain and inhibit GEF activity and that ULK phosphorylation might release this auto-inhibition. Using...