Vps34 Kinase Domain Dynamics Regulate the Autophagic PI 3-Kinase Complex

Stjepanović, Goran; Baskaran, Sulochanadevi; Lin, Mary Grace; Hurley, James H.

doi:10.1016/j.molcel.2017.07.003

Cited by 90 publications

(86 citation statements)

References 55 publications

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“…Mechanistic work indicates that the SAC1 domain of Synj1 is needed to dephosphorylate PI(3)P, and likely also PI(3,5)P 2 , on synaptic The EMBO Journal 37: e98960 | 2018 autophagosomal membranes (Vanhauwaert et al, 2017). These phosphoinositides, produced by Vps34 and Fab1, respectively, are critically required during the initial steps, and likely in the maturation steps, of autophagy (Rusten et al, 2007;Juhász et al, 2008;Thoresen et al, 2010;Stjepanovic et al, 2017). However, as the autophagosome matures, these phosphoinositides need to be dephosphorylated to lower the affinity of specific autophagic factors such as Atg18a/WIPI2, allowing autophagosome formation to move forward.…”

Section: Synj1mentioning

confidence: 99%

Parkinson's disease: convergence on synaptic homeostasis

2018

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Parkinson's disease, the second most common neurodegenerative disorder, affects millions of people globally. There is no cure, and its prevalence will double by 2030. In recent years, numerous causative genes and risk factors for Parkinson's disease have been identified and more than half appear to function at the synapse. Subtle synaptic defects are thought to precede blunt neuronal death, but the mechanisms that are dysfunctional at synapses are only now being unraveled. Here, we review recent work and propose a model where different Parkinson proteins interact in a cell compartment-specific manner at the synapse where these proteins regulate endocytosis and autophagy. While this field is only recently emerging, the work suggests that the loss of synaptic homeostasis may contribute to neurodegeneration and is a key player in Parkinson's disease.

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Section: Synj1mentioning

confidence: 99%

Parkinson's disease: convergence on synaptic homeostasis

2018

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“…Recruitment of a complex containing Vps34 is an important early step in autophagy and phagocytosis, although complexes of different compositions are associated with each. In the canonical autophagy pathway, cellular stress activates the ULK1 complex, which in turn activates the PI3KC3 complex I, containing the scaffold protein Vps15, Atg14, Beclin 1 and the type III phosphoinositide 3-kinase, Vps34 (Stjepanovic et al, 2017); this activation leads to extension of a double-membrane phagophore enriched in PI(3)P (Axe et al, 2008;Hayashi-Nishino et al, 2009;Itakura and…”

Section: Introductionmentioning

confidence: 99%

Multiple phosphatidylinositol(3)phosphate roles in retinal pigment epithelium membrane recycling

et al. 2020

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The low-abundance lipid phosphatidylinositol-3-phosphate (PI(3)P) is important for membrane dynamics in autophagy, endosome processing, and phagocytosis. In retinal pigmented epithelial cells (RPE) all three pathways are important, but phagocytosis of disk membranes shed from adjacent photoreceptors is especially important for ensuring health of photoreceptors and preventing retinal degeneration. By eliminating Vps34, the kinase responsible for synthesizing PI(3)P in RPE, we have found that PI(3)P plays distinct roles in each pathway. In phagocytosis it is not required for disk engulfment or phagosome transport but is essential for recruitment and lipidation of LC3. In contrast, initiation of autophagy and LC3 recruitment to autophagosomes does not require PI(3)P, which can be bypassed by an alternative mechanism of ATG16L recruitment that does not require PI(3)P, Rab11a, or WIPI2. In all three pathways, PI(3)P is essential for fusion with lysosomes; autophagosomes, phagosomes, and Rab7-positive late endosomes, as well as enlarged lysosomes, accumulate in large numbers in the absence of Vps34, leading to cell death.

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“…The kinase domain of VPS15 keeps basal activity low by restricting the activation loop of VPS34 (12). Our laboratory previously found that the VPS34 kinase domain is highly dynamic (11,27). We found that "leashing" the VPS34 kinase domain to the VPS15 kinase domain with a 12-residue linker blocked even basal kinase activity (Stjepanovic et al, 2017).…”

Section: Discussionmentioning

confidence: 78%

“…Our laboratory previously found that the VPS34 kinase domain is highly dynamic (11,27). We found that "leashing" the VPS34 kinase domain to the VPS15 kinase domain with a 12-residue linker blocked even basal kinase activity (Stjepanovic et al, 2017). This showed that a substantial structural change relative to the published PI3KC3-C2 conformation was essential for any activity, yet the precise nature of the structural change was not clear.…”

Section: Discussionmentioning

confidence: 96%

“…Even when preferred orientations can be reduced or eliminated, the dynamics of the catalytic right arm of the complex (27) has still limited analysis (14). The apparent reduction in dynamics in the BECN1-NRBF2 MIT form of PI3KC3-C1 suggested that this sample might be more tractable to cryo-EM than the wild-type PI3KC3-C1 and -C2 complexes.…”

Section: Cryo-em Structure Of the Becn1-mit-fusion Complexmentioning

confidence: 99%

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Structural Pathway for Allosteric Activation of the Autophagic PI 3-Kinase Complex I

Young

Goerdeler

Hurley

2019

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Autophagy induction by starvation and stress involves the enzymatic activation of the class III phosphatidylinositol 3-kinase complex I (PI3KC3-C1). The inactive basal state of PI3KC3-C1 is maintained by inhibitory contacts between the VPS15 protein kinase and VPS34 lipid kinase domains that restrict the conformation of the VPS34 activation loop. Here, the pro-autophagic MIT domain-containing protein NRBF2 was used to map the structural changes leading to activation. Cryo-EM was used to visualize stepwise PI3KC3-C1 activating effects of binding the NRFB2 MIT domains. Binding of a single NRBF2 MIT domain to bends the helical solenoid of the VPS15 scaffold, displaces the protein kinase domain of VPS15, and releases the VPS34 kinase domain from the inhibited conformation. Binding of a second MIT stabilizes the VPS34 lipid kinase domain in an active conformation that has an unrestricted activation loop and is poised for access to membranes.Autophagy is a core cellular process, conserved throughout eukaryotes, which is the central recycling system for the removal of misfolded proteins, damaged organelles, and the recycling of nutrients in starvation. Autophagic dysfunction is implicated in many disease states, including neurodegeneration, immune disorders, cancer, and aging, among others (1). The class III phosphatidylinositol-3 kinase complexes (PI3KC3) I and II (PI3KC3-C1 and -C2), respectively, are essential for the initiation and expansion of autophagosomes (2-5). PI3KC3 generates the lipid phosphatidylinositol-3-phosphate, PI(3)P, which is recognized by the WIPI proteins. WIPIs in turn recruit the machinery that conjugates the autophagosomal marker LC3 to the expanding autophagosomal membrane (6). PI3KC3-C1 has been proposed to be a promising therapeutic target for autophagy activators (7) because the generation of PI(3)P is absolutely required for the recruitment of downstream autophagy proteins. There is considerable medical interest in selectively activating this pathway to promote human health and treat disease, yet there are no FDA approved pharmaceuticals that uniquely activate autophagy.PI3KC3-C1 consists of the lipid kinase VPS34, the putative serine/threonine protein kinase VPS15, the regulatory subunit BECN1, and the early autophagy-specific targeting subunit ATG14 (8,9). In PI3KC3-C2, ATG14 is replaced with UVRAG (10), while the other three subunits are preserved. The overall architecture of both PI3KC3-C1 and -C2 has the shape of the letter V (11, 12) (Fig. 1A). The long coiled-coils of BECN1 and ATG14 scaffold the left arm in the standard view, with the membrane binding BARA domain of BECN1 located at the outermost tip of the arm. PI3KC3-C2 is inhibited by Rubicon and the HIV-1 protein Nef (13-15), which regulate membrane docking by the tip of the left arm. The catalytic domains of the kinases VPS34 and VPS15 are at the tip of the right arm (11,12). PI3KC3 complexes are phosphoregulated by the Unc-51 like autophagy-activating kinase 1 (ULK1) complex (16),

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Vps34 Kinase Domain Dynamics Regulate the Autophagic PI 3-Kinase Complex

Cited by 90 publications

References 55 publications

Parkinson's disease: convergence on synaptic homeostasis

Parkinson's disease: convergence on synaptic homeostasis

Multiple phosphatidylinositol(3)phosphate roles in retinal pigment epithelium membrane recycling

Structural Pathway for Allosteric Activation of the Autophagic PI 3-Kinase Complex I

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