Vacuolar-type H⁺- ATPase (v-ATPase), a multi-subunit protein complex, has two distinct functions on lysosomes: acidifying the lysosomal lumen and controlling mTOR-S6K (mTORC1) signaling, both of which are crucial for several biological processes. However, little is known about how both functions of v-ATPase are coordinated and whether lysosomes are also involved in mTOR-AKT (mTORC2) signaling. We found that knocking down (KD) of a subunit of v-ATPase impairs cell proliferation of undifferentiated induced pluripotent stem cells (iPSCs) although all cells do not die. As expected, lysosomal pH increased and mTORC1 signaling was attenuated in the KD cells. Unexpectedly, mTORC2 signaling was also impaired. Treatment of iPSCs with bafilomycin A1, a specific inhibitor of v-ATPase proton pump, increased lysosomal pH, and impaired both mTORC1 and mTORC2 signaling pathways. When treating Hek293, a cancer cell line, with the inhibitor, attenuation of mTORC2 activity was observed. Therefore, in addition to mTORC1, v-ATPase regulates the mTORC2 activity. We are now investigating how the proton pump affects the mTOR signaling using deletion mutants of the subunit and some chemicals that affect pH in lysosomes. We will discuss our results in this meeting.