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Lysosomal metabolomics reveals V-ATPase- and mTOR-dependent regulation of amino acid efflux from lysosomes

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Science  10 Nov 2017:
Vol. 358, Issue 6364, pp. 807-813
DOI: 10.1126/science.aan6298

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Regulated lysosomal efflux of amino acids

A new technique allows rapid purification of lysosomes and metabolic profiling by liquid chromatography and mass spectrometry. Abu-Remaileh et al. engineered cultured human cells to produce a protein tag on lysosomal membranes that could be used to rapidly precipitate purified lysosomes on magnetic beads. Analysis of their contents under various conditions showed that efflux from the lysosome of most essential amino acids (but not that of most other amino acids) is a regulated process. Amino acid transport was inhibited under conditions of nutrient depletion as a result of inhibition of the mTOR (mechanistic target of rapamycin) protein kinase complex.

Science, this issue p. 807

Abstract

The lysosome degrades and recycles macromolecules, signals to the cytosol and nucleus, and is implicated in many diseases. Here, we describe a method for the rapid isolation of mammalian lysosomes and use it to quantitatively profile lysosomal metabolites under various cell states. Under nutrient-replete conditions, many lysosomal amino acids are in rapid exchange with those in the cytosol. Loss of lysosomal acidification through inhibition of the vacuolar H+–adenosine triphosphatase (V-ATPase) increased the luminal concentrations of most metabolites but had no effect on those of the majority of essential amino acids. Instead, nutrient starvation regulates the lysosomal concentrations of these amino acids, an effect we traced to regulation of the mechanistic target of rapamycin (mTOR) pathway. Inhibition of mTOR strongly reduced the lysosomal efflux of most essential amino acids, converting the lysosome into a cellular depot for them. These results reveal the dynamic nature of lysosomal metabolites and that V-ATPase- and mTOR-dependent mechanisms exist for controlling lysosomal amino acid efflux.

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