Autophagy-dependent and -independent roles of ATG1 in the coordination of cell differentiation, cell survival and cell death

Saccharomyces cerevisiae has evolved distinct mechanisms to tolerate suboptimal conditions. One well-studied example is the varied response to the duration and degree of nitrogen starvation. In moderately low concentrations of nitrogen diploid cells undergo a morphological transition from unattached oval yeast cells to elongated attached chains of cells or pseudohyphae that presumably forage for additional sources of nitrogen. By contrast, prolonged exposure to extremely low nitrogen causes fewer cells within a colony to switch to pseudohyphae instead utilizing a more extreme mechanism for survival: digestion of internal macromolecules and organelles to produce additional nitrogen sources via autophagy. Thus, cells must gauge the levels of nitrogen availability and then coordinate the final physiological output to activate either the anabolic processes of protein translation and modifications required for pseudohyphal growth or the catabolic processes needed for autophagic protein degradation. Previous reports suggest that activation of either mechanism represses the other however the specific crosstalk between autophagy and pseudohyphal growth has not been elucidated.; Here we demonstrate that ATG1, a ser/thr kinase required for autophagy activity, is also essential for proper pseudohyphal growth. This novel function is dependant on a functional kinase domain and independent of autophagy. ATG1 also functions upstream of several pseudohyphae master transcriptional regulators including TEC1, MGA1 and FLO8. The discovery that ATG1 is a key component of both autophagy and pseudohyphae suggests that ATG1 plays a key dual role in the morphological and physiological switch required to ensure cell survival in suboptimal conditions. We demonstrate that the ATG1ox phenotype is directly proportionate to the concentration of nitrogen, unlike other pseudohyphae specific components, suggesting that the nitrogen dependant signals control the extent of ATG1ox dependent switch. To elucidate the regulation of the proposed switch, we identified several kinases capable of phosphorylating ATG1 in vitro including KSS1, FUS3, SWE1 and TPK3---all known regulators of pseudohyphal growth. Genetically, ATG1 is downstream of KSS1/FUS3 and other MAPK components responsible for pseudohyphal growth. Most significantly we show that the KSS1 can negatively regulate autophagy when the MAPK cascade is activated, thus demonstrating that activation of the MAPK cascade activates pseudohyphae development and can inhibit autophagy. Taken together our data suggests that ATG1 may be a nitrogen-dependant input-output switch during starvation conditions: in moderately low nitrogen conditions the activated KSS1 phosphorylates ATG1 to initiate pseudohyphae growth while minimizing autophagy however in the extremely low nitrogen conditions mTOR mediated dephosphorylation of ATG1 switches development to activate autophagy while minimizing pseudohyphal growth.