インサイト - Molecular Biology - # Autophagy Initiation Mechanism

Structural Basis and Mechanism of ULK Complex Formation for Autophagy Initiation in Mammals

Q: What are the potential tissue-specific or context-dependent regulatory mechanisms that modulate the triadic ULK1-ATG13-FIP200 interactions to fine-tune autophagy activity in different cellular and physiological contexts?

The regulation of the triadic ULK1-ATG13-FIP200 interactions is likely influenced by several tissue-specific and context-dependent mechanisms that ensure autophagy is appropriately modulated according to cellular needs. One potential mechanism involves the differential expression of splicing variants of ATG13, which can alter the binding affinity and interaction dynamics with ULK1 and FIP200. For instance, specific isoforms may lack critical interaction motifs, thereby reducing the stability of the ULK complex and subsequently affecting autophagic flux. Additionally, post-translational modifications (PTMs) such as phosphorylation, ubiquitination, or acetylation of ULK1, ATG13, or FIP200 can modulate their interactions. For example, mTOR signaling, which is known to phosphorylate ULK1, can influence the assembly of the ULK complex in response to nutrient availability, thereby linking autophagy regulation to metabolic states. Furthermore, cellular stress conditions, such as oxidative stress or nutrient deprivation, can induce changes in the localization and abundance of these proteins, affecting their interactions. The presence of specific signaling molecules or metabolites in different tissues may also dictate the assembly or disassembly of the ULK complex, allowing for a tailored autophagic response that meets the physiological demands of various cell types.

Q: How do the structural differences between the mammalian ULK complex and the yeast Atg1 complex, such as the 1:1:2 versus the bridging interactions, contribute to the distinct mechanisms of autophagosome formation site organization and regulation?

The structural differences between the mammalian ULK complex and the yeast Atg1 complex are pivotal in determining their respective mechanisms of autophagosome formation. In the mammalian ULK complex, the 1:1:2 stoichiometry, where one ATG13 binds to two FIP200 molecules, allows for a stable and robust assembly of the ULK complex. This configuration facilitates direct interactions among ULK1, ATG13, and FIP200, which are essential for the initiation of autophagy. The inability of ATG13 to bridge FIP200 dimers means that the ULK complex does not form higher-order assemblies as seen in yeast, where Atg13 can connect multiple Atg17 dimers, promoting a more dynamic and potentially larger assembly. In contrast, the bridging interactions in the yeast Atg1 complex enable a higher-order organization that may enhance the efficiency of autophagosome formation. This structural arrangement allows for the rapid recruitment of additional autophagy-related proteins and the formation of a larger autophagic machinery on the vacuolar membrane. The distinct structural configurations thus reflect evolutionary adaptations to the specific cellular environments and regulatory needs of mammals versus yeast, influencing how autophagy is initiated and regulated in response to various stimuli.

Q: Could the structural insights from this study be leveraged to develop pharmacological interventions that selectively target the ULK complex assembly or disassembly to modulate autophagy for therapeutic purposes?

Yes, the structural insights gained from this study provide a valuable foundation for developing pharmacological interventions aimed at selectively targeting the assembly or disassembly of the ULK complex. By understanding the specific interactions between ULK1, ATG13, and FIP200, researchers can design small molecules or peptides that either stabilize or disrupt these interactions. For instance, compounds that mimic the binding sites of ATG13 or FIP200 could enhance the stability of the ULK complex, potentially boosting autophagic activity in conditions where enhanced autophagy is beneficial, such as in neurodegenerative diseases or cancer therapy. Conversely, inhibitors that disrupt the ULK1-ATG13 or ATG13-FIP200 interactions could be developed to reduce autophagy in contexts where it is detrimental, such as in certain metabolic disorders or during excessive autophagic activity leading to cell death. Additionally, the identification of specific post-translational modification sites that regulate these interactions could lead to the development of drugs that modulate the activity of kinases or phosphatases involved in these processes, providing another layer of control over autophagy. Overall, leveraging the structural details of the ULK complex opens new avenues for targeted therapies that can fine-tune autophagic processes in various diseases.

核心概念

The triadic interaction among ULK1, ATG13, and FIP200 is crucial for the formation and function of the ULK complex, which initiates autophagosome formation in mammals.

要約

The study used AlphaFold2 to predict the structure of the ULK1-ATG13-FIP200 complex and confirmed the predicted interactions through in vitro and in vivo mutational analyses. The key findings are:

ATG13 binds to two FIP200 molecules within the same FIP200 dimer using two phenylalanine residues, forming a 1:1:2 stoichiometry of the ULK1-ATG13-FIP200 complex.
ATG13 binds to the tandem MIT domains of ULK1 through a MIT-MIM interaction, similar to the yeast Atg1-Atg13 complex.
ULK1 also directly interacts with FIP200 through its MIT domains, and this direct interaction is partially important for autophagy function, in addition to the indirect interaction via ATG13.
Disrupting any of the three interactions (ATG13-FIP200, ATG13-ULK1, ULK1-FIP200) results in a partial reduction in autophagy activity, indicating the complementary and crucial nature of the triadic interactions for robust ULK complex formation and autophagy initiation.

The study provides structural insights into the mechanism of ULK complex assembly and organization, which is essential for understanding the regulation of autophagy initiation in mammals.

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biorxiv.org

統計

The predicted buried surface area between FIP200A and FIP200B is 3,658 Å2.
The predicted buried surface area between FIP200A and ATG13 is 2,195 Å2.
The predicted buried surface area between FIP200B and ATG13 is 1,966 Å2.
The predicted buried surface area between ATG13 and ULK1 is 2,140 Å2.
The predicted buried surface area between FIP200A and ULK1 is 1,681 Å2.
The dissociation constant (Kd) for the interaction between FIP200 (1-634) and ATG13 (363-517) is 6.6 μM.
The dissociation constant (Kd) for the interaction between ULK1 (636-1050) and ATG13 (363-517) is 0.34 μM.

引用

"The triadic interaction of ULK1, ATG13, and FIP200 is crucial for autophagosome formation and provide a structural basis and insights into the regulation mechanism of autophagy initiation in mammals."
"The ULK1–ATG13–FIP200 triadic interaction is crucial for autophagy initiation and provide a structural basis and insights into the regulation mechanism of autophagy initiation in mammals."

抽出されたキーインサイト

The triad interaction of ULK1, ATG13, and FIP200 is required for ULK complex formation and autophagy

by Hama,Y., Fuj... 場所 www.biorxiv.org 08-02-2024

https://www.biorxiv.org/content/10.1101/2024.08.02.606296v2

深掘り質問

What are the potential tissue-specific or context-dependent regulatory mechanisms that modulate the triadic ULK1-ATG13-FIP200 interactions to fine-tune autophagy activity in different cellular and physiological contexts?

The regulation of the triadic ULK1-ATG13-FIP200 interactions is likely influenced by several tissue-specific and context-dependent mechanisms that ensure autophagy is appropriately modulated according to cellular needs. One potential mechanism involves the differential expression of splicing variants of ATG13, which can alter the binding affinity and interaction dynamics with ULK1 and FIP200. For instance, specific isoforms may lack critical interaction motifs, thereby reducing the stability of the ULK complex and subsequently affecting autophagic flux.
Additionally, post-translational modifications (PTMs) such as phosphorylation, ubiquitination, or acetylation of ULK1, ATG13, or FIP200 can modulate their interactions. For example, mTOR signaling, which is known to phosphorylate ULK1, can influence the assembly of the ULK complex in response to nutrient availability, thereby linking autophagy regulation to metabolic states.
Furthermore, cellular stress conditions, such as oxidative stress or nutrient deprivation, can induce changes in the localization and abundance of these proteins, affecting their interactions. The presence of specific signaling molecules or metabolites in different tissues may also dictate the assembly or disassembly of the ULK complex, allowing for a tailored autophagic response that meets the physiological demands of various cell types.

How do the structural differences between the mammalian ULK complex and the yeast Atg1 complex, such as the 1:1:2 versus the bridging interactions, contribute to the distinct mechanisms of autophagosome formation site organization and regulation?

The structural differences between the mammalian ULK complex and the yeast Atg1 complex are pivotal in determining their respective mechanisms of autophagosome formation. In the mammalian ULK complex, the 1:1:2 stoichiometry, where one ATG13 binds to two FIP200 molecules, allows for a stable and robust assembly of the ULK complex. This configuration facilitates direct interactions among ULK1, ATG13, and FIP200, which are essential for the initiation of autophagy. The inability of ATG13 to bridge FIP200 dimers means that the ULK complex does not form higher-order assemblies as seen in yeast, where Atg13 can connect multiple Atg17 dimers, promoting a more dynamic and potentially larger assembly.
In contrast, the bridging interactions in the yeast Atg1 complex enable a higher-order organization that may enhance the efficiency of autophagosome formation. This structural arrangement allows for the rapid recruitment of additional autophagy-related proteins and the formation of a larger autophagic machinery on the vacuolar membrane. The distinct structural configurations thus reflect evolutionary adaptations to the specific cellular environments and regulatory needs of mammals versus yeast, influencing how autophagy is initiated and regulated in response to various stimuli.

Could the structural insights from this study be leveraged to develop pharmacological interventions that selectively target the ULK complex assembly or disassembly to modulate autophagy for therapeutic purposes?

Yes, the structural insights gained from this study provide a valuable foundation for developing pharmacological interventions aimed at selectively targeting the assembly or disassembly of the ULK complex. By understanding the specific interactions between ULK1, ATG13, and FIP200, researchers can design small molecules or peptides that either stabilize or disrupt these interactions.
For instance, compounds that mimic the binding sites of ATG13 or FIP200 could enhance the stability of the ULK complex, potentially boosting autophagic activity in conditions where enhanced autophagy is beneficial, such as in neurodegenerative diseases or cancer therapy. Conversely, inhibitors that disrupt the ULK1-ATG13 or ATG13-FIP200 interactions could be developed to reduce autophagy in contexts where it is detrimental, such as in certain metabolic disorders or during excessive autophagic activity leading to cell death.
Additionally, the identification of specific post-translational modification sites that regulate these interactions could lead to the development of drugs that modulate the activity of kinases or phosphatases involved in these processes, providing another layer of control over autophagy. Overall, leveraging the structural details of the ULK complex opens new avenues for targeted therapies that can fine-tune autophagic processes in various diseases.