Identification of Atg3 as an intrinsically disordered polypeptide yields insights into the molecular dynamics of autophagy-related proteins in yeast

Popelka, Hana; Uversky, Vladimir N.; Klionsky, Daniel J.

doi:10.4161/auto.28616

Cited by 39 publications

(31 citation statements)

References 62 publications

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“…We interpret this to mean that only the fully dislodged conformation is maximally active. It has been widely noted that autophagy complexes are rich in intrinsically disordered regions (Hurley and Schulman, 2014; Mei et al, 2016; Popelka et al, 2014; Yamamoto et al, 2016). The key role of complete dislodging in the activation of PI3KC3 highlights how critical it is that there be a long linker between the VPS34 C2 and HELCAT regions.…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2017

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Summary The class III phosphatidylinositol 3-kinase complex I (PI3KC3-C1) is required for the initiation of essentially all macroautophagic processes. PI3KC3-C1 consists of the lipid kinase catalytic subunit VPS34, the VPS15 scaffold, and the regulatory BECN1 and ATG14 subunits. The VPS34 catalytic domain and BECN1:ATG14 subcomplex do not touch, and it is unclear how allosteric signals are transmitted to VPS34. We used EM and cross-linking mass spectrometry to dissect five conformational substates of the complex, including one in which the VPS34 catalytic domain is dislodged from the complex but remains tethered by an intrinsically disordered linker. A “leashed” construct prevented dislodging without interfering with the other conformations, blocked enzyme activity in vitro, and blocked autophagy induction in yeast cells. This pinpoints the dislodging and tethering of the VPS34 catalytic domain, and its regulation by VPS15, as a master allosteric switch in autophagy induction.

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Section: Discussionmentioning

confidence: 99%

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

et al. 2017

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“…Recent work has highlighted the important role IDRs have in autophagy regulation. 44,45 Common to the IDRs of Atg29 and the Atg13 [CTD] is the presence of a large number of putative phosphorylation sites. As Atg13 dephosphorylation and Atg29 phosphorylation are required for the initiation of autophagy, these IDRs might mediate transient and selective interactions required for complex formation and/or recruitment of other Atg proteins essential to the execution of autophagy initiation.…”

Section: Discussionmentioning

confidence: 99%

Molecular interactions of theSaccharomyces cerevisiaeAtg1 complex provide insights into assembly and regulatory mechanisms

Chew¹,

Liu³

et al. 2015

Autophagy

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(2015) Molecular interactions of the Saccharomyces cerevisiae Atg1 complex provide insights into assembly and regulatory mechanisms, Autophagy, 11:6, 891-905, DOI: 10.1080/15548627.2015 The Atg1 complex, which contains 5 major subunits: Atg1, Atg13, Atg17, Atg29, and Atg31, regulates the induction of autophagy and autophagosome formation. To gain a better understanding of the overall architecture and assembly mechanism of this essential autophagy regulatory complex, we have reconstituted a core assembly of the Saccharomyces cerevisiae Atg1 complex composed of full-length Atg17, Atg29, and Atg31, along with the C-terminal domains of Atg1 (Atg1 [CTD]) and Atg13 (Atg13 [CTD]). Using chemical-crosslinking coupled with mass spectrometry (CXMS) analysis we systematically mapped the intersubunit interaction interfaces within this complex. Our data revealed that the intrinsically unstructured C-terminal domain of Atg29 interacts directly with Atg17, whereas Atg17 interacts with Atg13 in 2 distinct intrinsically unstructured regions, including a previously unknown motif that encompasses several putative phosphorylation sites. The Atg1[CTD] crosslinks exclusively to the Atg13[CTD] and does not appear to make direct contact with the Atg17-Atg31-Atg29 scaffold. Finally, single-particle electron microscopy analysis revealed that both the Atg13[CTD] and Atg1 [CTD] localize to the tip regions of Atg17-Atg31-Atg29 and do not alter the distinct curvature of this scaffolding subcomplex. This work provides a comprehensive understanding of the subunit interactions in the fully assembled Atg1 core complex, and uncovers the potential role of intrinsically disordered regions in regulating complex integrity.

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“…In recent years, an increasing amount of crystallographic data of the autophagy-related proteins has been reported, which is providing valuable information to elucidate the mechanism of the autophagic machinery [74]. Furthermore, there is a growing awareness of the importance of intrinsically disordered regions in terms of regulating protein function and protein-protein interaction including those within Atg proteins [75, 76]. Here, we discuss some representative components of the core autophagy machinery at both structural and molecular levels, connecting the structure with the molecular mechanism of the autophagy core machinery.…”

Section: Structure Function and Modification Of The Core Autophagmentioning

confidence: 99%

An overview of macroautophagy in yeast

Wen

Klionsky

2016

Journal of Molecular Biology

230

188

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Macroautophagy is an evolutionarily conserved dynamic pathway that functions primarily in a degradative manner. A basal level of macroautophagy occurs constitutively, but this process can be further induced in response to various types of stress including starvation, hypoxia and hormonal stimuli. The general principle behind macroautophagy is that cytoplasmic contents can be sequestered within a transient double-membrane organelle, an autophagosome, which subsequently fuses with a lysosome or vacuole (in mammals, or yeast and plants, respectively), allowing degradation of the cargo followed by recycling of the resulting macromolecules. Through this basic mechanism, macroautophagy has a critical role in cellular homeostasis; however, either insufficient or excessive macroautophagy can seriously compromise cell physiology, and thus it needs to be properly regulated. In fact, a wide range of diseases is associated with dysregulation of macroautophagy. There has been substantial progress in understanding the regulation and molecular mechanisms of macroautophagy in different organisms; however, many questions concerning some most fundamental aspects of macroautophagy still remain unresolved. In this review, we summarize current knowledge about macroautophagy mainly in yeast, including the mechanism of autophagosome biogenesis, the function of the core macroautophagic machinery, the regulation of macroautophagy, and the process of cargo recognition in selective macroautophagy, with the goal of providing insights into some of the key unanswered questions in this field.

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Identification of Atg3 as an intrinsically disordered polypeptide yields insights into the molecular dynamics of autophagy-related proteins in yeast

Cited by 39 publications

References 62 publications

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

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

Molecular interactions of theSaccharomyces cerevisiaeAtg1 complex provide insights into assembly and regulatory mechanisms

An overview of macroautophagy in yeast

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