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Signalling by mammalian target of rapamycin (mTOR) as part of the mTOR complex 1 (mTORC1) regulates a wide range of cellular processes, including cell growth and division, through its ability to sense nutrients and energy signals. Two recent studies provide examples of how the localization of mTOR determines its function and activity. One study shows that mTOR regulates an ATP-sensitive Na+ channel on endolysosomes (the product of endosome–lysosome fusion), and the other reveals how mTORC1 is sequestered at stress granules by dual specificity Tyr phosphorylation-regulated kinase 3 (DYRK3).

In the first study, Cang et al. sought to determine how endosomes and lysosomes detect cytosolic ATP levels to couple the availability of nutrients and cellular responses. They found that endolysosomes from mouse peritoneal macrophages have an endolysosomal ATP-sensitive Na+-permeable channel (lysoNaATP) that responds to changes in ATP levels. Further experiments revealed that this channel comprises TPC1 (two pore calcium channel 1) and TPC2, and that the flow of Na+ through lysoNaATP is inhibited by ATP concentrations that occur when cells have sufficient nutrients.

Two recent studies provide examples of how the localization of mTOR determines its function and activity.

Next, the authors assessed how lysoNaATP senses ATP. They observed that the depletion or inhibition of mTOR, which is known to be tethered to lysosomal membranes, reduced the sensitivity of lysoNaATP to ATP. Furthermore, mTOR interacted with TPC1 and TPC2, and its overexpression enhanced the sensitivity of lysoNaATP to ATP; this was dependent on the kinase activity of mTOR. It is known that mTOR translocates away from lysosomes when amino acids are depleted. In this study, the withdrawal of amino acids from cells prevented the inhibition of lysoNaATP by ATP, although lysoNaATP was inhibited even in the absence of ATP when mTOR was forcibly retained on lysosomes. Thus, lysoNaATP is inhibited (and thus closed) by mTOR when there are sufficient nutrients, but opens in the absence of ATP because mTOR dissociates from the endolysosome. The authors found that this enables the channel to correctly regulate endolysosomal membrane potential and pH.

Wippich et al. focused on stress granules, which are dense aggregations of proteins and RNAs that appear in the cytosol in times of cellular stress. To gain insight into how the dissolution of stress granules is regulated, they assessed them in the presence of different kinase inhibitors and observed that inhibition of DYRK family members stabilized them. Further experiments revealed that DYRK3 localizes to stress granules in response to oxidative and osmotic stress and confirmed that these structures are stabilized in the absence of DYRK3 kinase activity.

So what are the effects of kinase inactive DYRK3-mediated stabilization of stress granules? Inhibiting DYRK3 decreased the kinase activity of mTOR when it was part of mTORC1, suggesting that DYRK3 kinase activity is required for active mTORC1. Further experiments showed that mTOR is recruited to and sequestered at stress granules in response to cellular stress, as is the mTORC1-specific subunit RAPTOR. Inducing the dissolution of stress granules in the presence of a DYRK3 inhibitor enhanced mTORC1 activity but did not completely restore it, suggesting that DYRK3-inhibition reduces mTORC1 activity by a second mechanism. Indeed, uninhibited DYRK3 was found to phosphorylate PRAS40, a negative regulator of mTORC1, to promote mTORC1 activity. Thus, in times of stress, kinase inactive DYRK3 inhibits mTORC1 by stabilizing stress granules to sequester mTOR and RAPTOR and by failing to release the inhibitory hold that PRAS40 has on mTORC1. Under homeostatic conditions, kinase active DYRK3 leads to the dissolution of stress granules to promote the cytosolic localization of mTORC1 and 'neutralizes' the mTORC1 inhibitor PRAS40. Importantly, the authors also found that DYRK3 cycles between stress granules and the cytosol and that its cytosolic localization depends on its kinase activity.

These exciting studies further highlight how location is key in determining mTOR action.