Regulation of human mTOR complexes by DEPTOR.

Matthias Wälchli,Karolin Berneiser,Timm Maier,Stefan Imseng,Louise-Marie Craigie,Michael N Hall,Edward Stuttfeld,Francesca Mangia

doi:10.7554/elife.70871

Abstract

The vertebrate-specific DEP domain-containing mTOR interacting protein (DEPTOR), an oncoprotein or tumor suppressor, has important roles in metabolism, immunity, and cancer. It is the only protein that binds and regulates both complexes of mammalian target of rapamycin (mTOR), a central regulator of cell growth. Biochemical analysis and cryo-EM reconstructions of DEPTOR bound to human mTOR complex 1 (mTORC1) and mTORC2 reveal that both structured regions of DEPTOR, the PDZ domain and the DEP domain tandem (DEPt), are involved in mTOR interaction. The PDZ domain binds tightly with mildly activating effect, but then acts as an anchor for DEPt association that allosterically suppresses mTOR activation. The binding interfaces of the PDZ domain and DEPt also support further regulation by other signaling pathways. A separate, substrate-like mode of interaction for DEPTOR phosphorylation by mTOR complexes rationalizes inhibition of non-stimulated mTOR activity at higher DEPTOR concentrations. The multifaceted interplay between DEPTOR and mTOR provides a basis for understanding the divergent roles of DEPTOR in physiology and opens new routes for targeting the mTOR-DEPTOR interaction in disease.

Highlights

Our structural and mutational analyses suggest a model for DEPTOR action on mammalian target of rapamycin (mTOR) complexes, in which DEPTOR provides an additional layer of control with the ability to stimulate or inhibit the mTOR complexes (Figure 4a)
DEPTOR partially inhibits mTOR activity by a dominant negative effect of DEPt association or moderately stimulates mTOR activity via the influence of the PDZ domain, if DEPt is prevented from mTOR association by phosphatidic acid (PA) binding (Figure 4b)
A suppression of non-s timulated basal mTOR complex 1 (mTORC1) or mTOR complex 2 (mTORC2) would only be observed at high concentration of DEPTOR (Figure 4b) that result in additional substrate-like binding of DEPTOR to mTORCs

Summary

Introduction

DEP domain-containing mTOR interacting protein (DEPTOR), conserved in vertebrates, modulates the activity of the serine/threonine kinase mammalian target of rapamycin (mTOR), a master regulator of cell growth. mTOR acts in two functionally distinct multiprotein complexes, mTOR complex 1 (mTORC1) and mTORC2 (Sabatini et al, 1994; Jacinto et al, 2004; Sarbassov et al, 2004; Liu and Sabatini, 2020; Loewith and Hall, 2011; Loewith et al, 2002), and DEPTOR is the only protein reported to bind and inhibit both mTOR complexes (Peterson et al, 2009).DEPTOR is a 46 kDa protein comprising an N-terminal DEP (Dishevelled, Egl-10, and Pleckstrin) domain tandem, referred to as DEPt, and a C-terminal PDZ (postsynaptic density 95, disks large, zonula occludens-1) domain. DEP domain-containing mTOR interacting protein (DEPTOR), conserved in vertebrates, modulates the activity of the serine/threonine kinase mammalian target of rapamycin (mTOR), a master regulator of cell growth. The PDZ domain has been suggested to interact with mTOR (Peterson et al, 2009), and DEPt mediates phosphatidic acid (PA) binding (Weng et al, 2021). MTOR phosphorylates this motif, leading to subsequent additional phosphorylation, ubiquitylation by the SCFβTrCP E3 ubiquitin ligase, and DEPTOR degradation (Gao et al, 2011; Zhao et al, 2011; Duan et al, 2011). DEPTOR degradation, in turn, leads to activation of mTORC1 and inactivation of mTORC2 via the mTOR negative feedback loop. The interplay of mTOR and DEPTOR with the feedback loop from mTORC1 to mTORC2 and other signaling pathways leads to complex response patterns linked to variations in DEPTOR abundance depending on cell type and state (Caron et al, 2018; Catena and Fanciulli, 2017)

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Conclusion