The target of rapamycin (TOR) proteins regulate various cellular processes including autophagy1, which may play a protective role in certain neurodegenerative and infectious diseases2. Here we show that a primary small-molecule screen in yeast yields novel small-molecules modulators of mammalian autophagy. We first identified novel small-molecule enhancers (SMER) and inhibitors (SMIR) of the cytostatic effects of rapamycin in Saccharomyces cerevisiae. Three SMERs induced autophagy independently of rapamycin in mammalian cells, enhancing the clearance of autophagy substrates like mutant huntingtin and A53T α-synuclein, associated with Huntington's disease (HD) and familial Parkinson's disease, respectively3-5. These SMERs, which appear to act either independently, or downstream, of TOR, attenuated mutant huntingtin-fragment toxicity in HD cell and Drosophila models, suggesting therapeutic potential. We also screened structural analogs of these SMERs and identified additional candidate drugs enhancing autophagy. Thus, we have demonstrated proof-of-principle for a novel approach for discovery of small-molecule modulators of mammalian autophagy.The autophagy/lysosome and ubiquitin/proteasome pathways are the two major routes for protein clearance in eukaryotic cells. Proteasomes predominantly degrade short-lived nuclear and cytosolic proteins, which need to be unfolded to pass through the narrow pore of the proteasome barrel, precluding clearance of large membrane proteins and protein complexes (including oligomers and aggregates). Mammalian lysosomes, on the other hand, can degrade substrates like protein complexes and organelles. The bulk degradation of cytoplasmic proteins or organelles is largely mediated by macroautophagy, generally referred to as autophagy1. It involves the formation of double-membrane structures called 7 Joint corresponding authors. Correspondence to D.C. Rubinsztein -E-mail: dcr1000@cam.ac.uk , Telephone: (0)1223 762608, Fax: (0)1223 331206; S.L. Schreiber -E-mail: stuart_schreiber@harvard.edu. 6 These authors contributed equally to this work. Competing financial interestsThe authors declare no competing financial interests. Europe PMC Funders Group Europe PMC Funders Author ManuscriptsEurope PMC Funders Author Manuscripts autophagosomes/autophagic vacuoles (AVs), which fuse with lysosomes to form autolysosomes (also called autophagolysosomes) where their contents are then degraded by acidic lysosomal hydrolases. Autophagosomes are generated by elongation of small membrane structures, whose precise origins have yet to be elucidated1. Autophagy can be induced under physiological stress conditions such as starvation. Several protein kinases regulate autophagy, the best characterised being the mammalian target of rapamycin (mTOR), which negatively regulates the pathway in organisms from yeast to man1. However, the targets of mTOR-dependent and -independent signalling in the autophagy apparatus are not well understood in mammalian systems. Recently, we described an mTOR-independent path...

Global nucleosome occupancy in yeast

The presence of transcription factor-binding motifs is an important determinant of nucleosome depletion. Most motifs are associated with marked depletion only when they appear in combination, consistent with a model in which transcription factors act collaboratively to exclude nucleosomes and gain access to target sites in the DNA. In contrast, Rap1-binding sites cause marked depletion under steady-state conditions. We speculate that nucleosome depletion enables Rap1 to define chromatin domains and alter them in response to environmental cues.