Macroautophagy (hereafter autophagy) is a degradative cellular pathway that 
protects eukaryotic cells from stress, starvation, and microbial infection. This 
process must be tightly controlled because too little or too much autophagy can 
be deleterious to cellular physiology. The phosphatidylinositol (PtdIns) 
3-kinase Vps34 is a lipid kinase that regulates autophagy, but the role of other 
PtdIns kinases has not been examined. Here we demonstrate a role for PtdIns 
4-kinases and PtdIns4P 5-kinases in selective and nonselective types of 
autophagy in yeast. The PtdIns 4-kinase Pik1 is involved in Atg9 trafficking 
through the Golgi and is involved in both nonselective and selective types of 
autophagy, whereas the PtdIns4P 5-kinase Mss4 is specifically involved in 
mitophagy but not nonselective autophagy. Our data indicate that 
phosphoinositide kinases have multiple roles in the regulation of autophagic 
pathways.