Autophagy regulation by nutrient signaling

Abstract

The ability of cells to respond to changes in nutrient availability is essential for the maintenance of metabolic homeostasis and viability. One of the key cellular responses to nutrient withdrawal is the upregulation of autophagy. Recently, there has been a rapid expansion in our knowledge of the molecular mechanisms involved in the regulation of mammalian autophagy induction in response to depletion of key nutrients. Intracellular amino acids, ATP, and oxygen levels are intimately tied to the cellular balance of anabolic and catabolic processes. Signaling from key nutrient-sensitive kinases mTORC1 and AMP-activated protein kinase (AMPK) is essential for the nutrient sensing of the autophagy pathway. Recent advances have shown that the nutrient status of the cell is largely passed on to the autophagic machinery through the coordinated regulation of the ULK and VPS34 kinase complexes. Identification of extensive crosstalk and feedback loops converging on the regulation of ULK and VPS34 can be attributed to the importance of these kinases in autophagy induction and maintaining cellular homeostasis.

Figure 1

ATG protein recruitment in mammalian autophagosome formation. Temporal and functional relationship between ATG-protein complexes in autophagosome formation is depicted. These relationships were assembled from multiple independent studies to generate a working model with details summarized in the text. The core of VPS34 complexes, containing VPS34 and VPS15, is depicted as VPS34.

Figure 2

Upstream nutrient signaling to mTORC1 and AMPK. Nutrient starvation results in the inactivation of mTORC1. Oxygen or nutrient deficiency can activate AMPK through ADP:AMP accumulation, negatively regulating mTORC1 through either AMPK-mediated phosphorylation of mTORC1 or activation of the upstream repressor TSC. Limited oxygen also upregulates hypoxia-responsive genes, which are capable of suppressing mTORC1 signaling through the activation of TSC or inhibition of Rheb. Amino-acid withdrawal or inactivation of the PI3K pathway inhibits mTORC1 signaling through negatively regulating the activation of mTORC1 at the lysosome by Rag GTPases and Rheb.

Figure 3

Regulation of ULK1 and VPS34 complexes by nutrients and upstream kinases. Nutrient starvation activates ULK1 through AMPK-mediated phosphorylation or loss of mTORC1-mediated repression. Activation of ULK1 has been described to initiate a positive-feedback loop through the phosphorylation of the mTORC1 complex and a negative-feedback loop through the phosphorylation of AMPK. Activities of the core VPS34 complexes, containing VPS34 and VPS15 (depicted as VPS34 in all complexes), and Beclin-1-bound VPS34 are inhibited under starvation. AMPK-mediated repression of these complexes is caused by direct phosphorylation of the VPS34 catalytic subunit. Amino acid-induced activation of these complexes is mTORC1-dependent but not direct and does not involve ULK1 kinase. ATG14-containing VPS34 complexes are activated by AMPK or ULK1 through phosphorylation of Beclin-1 or can be inhibited by mTORC1-mediated phosphorylation of ATG14. UVRAG-containing VPS34 complexes are activated by AMPK-mediated phosphorylation of Beclin-1 in response to starvation. ULK1 phosphorylates AMBRA1, freeing VPS34 from the cytoskeleton to act at the phagophore. AMBRA1 acts in a positive-feedback loop with TRAF6 to promote ULK1 activation.

Figure 4

Regulation of VPS34 complex formation in response to nutrients. (A) Starvation activates JNK1 kinase, possibly through direct phosphorylation by AMPK. JNK1 phosphorylates Bcl-2, relieving Bcl-2-mediated repression of Beclin-1-VPS34 complexes. Bcl-2 may inhibit VPS34 complexes by disrupting Beclin-1-VPS34 interaction (left arrow) or by stabilizing an inactive Beclin-1 homodimeric complex (right arrow). (B) Hypoxia upregulates BNIP3 expression, which can bind Bcl-2, thereby relieving Bcl-2-mediated repression of Beclin-1-VPS34 complexes.