A Quantitative Ultrastructural Timeline of Nuclear Autophagy Reveals a Role for Dynamin-like Protein 1 at the Nuclear Envelope
Background Introduction
The nuclear envelope (NE) is a critical barrier between the nucleus and the cytoplasm, responsible for maintaining the stability of the nuclear environment. The integrity of the nuclear envelope is essential for normal cellular function, and its disruption is closely linked to aging and various diseases. Autophagy is a vital mechanism for degrading and recycling damaged or excess cellular components, including nucleophagy, where nuclear or nuclear envelope components are degraded via the autophagy pathway. However, the specific mechanisms of nucleophagy, particularly the molecular and ultrastructural processes of nuclear envelope remodeling, remain unclear.
Recent studies have shown that nucleophagy plays an important role in maintaining nuclear envelope homeostasis, but its molecular mechanisms and dynamic processes have not been fully elucidated. Specifically, how the inner nuclear membrane (INM) and outer nuclear membrane (ONM) are selectively removed through the autophagy pathway without compromising the integrity of the nuclear envelope remains a mystery. To address this, researchers used advanced microscopy techniques and molecular biology tools to uncover the quantitative timeline and key molecular mechanisms of nucleophagy.
Source of the Paper
This paper was authored by Philip J. Mannino, Andrew Perun, Ivan V. Surovtsev, and others from the Department of Cell Biology at Yale School of Medicine, and was published in Nature Cell Biology in March 2025. The research team employed four-dimensional lattice light sheet microscopy (4D LLSM) and correlative light and electron tomography (CLEM) to quantitatively describe the ultrastructural timeline of nucleophagy in yeast cells and revealed the non-canonical role of Dynamin-like protein 1 (Dnm1) in nuclear envelope remodeling.
Research Process and Results
1. Construction of the Nucleophagy Timeline
The research team first used fluorescently labeled nucleophagy receptor Atg39 to observe the dynamic process of nucleophagy in real-time via 4D lattice light sheet microscopy. The results showed that nucleophagy initiation involves the rapid accumulation of Atg39 on the nuclear envelope, with the entire process lasting approximately 300 seconds, ultimately delivering Atg39 and its cargo to the vacuole for degradation.
To further elucidate the ultrastructural details of nucleophagy, the researchers combined CLEM to observe morphological changes in the nuclear envelope during nucleophagy. They found that nucleophagy involves at least two consecutive membrane fission steps: first, the fission of the INM to form INM-derived vesicles (INMDVs) in the perinuclear space; second, the fission of the ONM to release double-membrane vesicles into the cytoplasm. Notably, ONM fission does not depend on phagophore engagement but relies on the activity of Dnm1.
2. The Key Role of Dnm1 in Nucleophagy
To validate the role of Dnm1 in nucleophagy, the researchers constructed yeast strains lacking Dnm1 and observed the dynamics of Atg39. The results showed that the absence of Dnm1 significantly reduced nucleophagic flux, particularly stalling the process after INM fission, preventing further progression. Further fluorescence microscopy and CLEM analysis revealed that the absence of Dnm1 led to the accumulation of INMDVs in the perinuclear space, unable to be released into the cytoplasm via ONM fission.
Additionally, the researchers found that the recruitment of Dnm1 depends on the autophagy scaffold protein Atg11. Through bimolecular fluorescence complementation (BiFC), they confirmed the direct interaction between Atg11 and Dnm1, further supporting the critical role of Dnm1 in nucleophagy.
3. Molecular Mechanism of Nucleophagy
Based on these findings, the researchers proposed a molecular mechanism model for nucleophagy: Atg39 first accumulates on the nuclear envelope and binds to the INM through its C-terminal amphipathic helices, forming INMDVs. Subsequently, Atg11 recruits Dnm1 to the nuclear envelope to catalyze ONM fission, releasing double-membrane vesicles into the cytoplasm. This process ensures the selective removal of nuclear envelope components while maintaining nuclear envelope integrity.
Conclusions and Significance
This study is the first to quantitatively describe the ultrastructural timeline of nucleophagy and reveal the non-canonical role of Dnm1 in nuclear envelope remodeling. The results demonstrate that nucleophagy ensures the selective removal of nuclear envelope components through two consecutive membrane fission steps while avoiding nuclear envelope disruption. This discovery not only deepens our understanding of the molecular mechanisms of nucleophagy but also provides new insights for research on aging and nuclear envelope-related diseases.
Research Highlights
- Quantitative Timeline: Using 4D lattice light sheet microscopy and CLEM, the study quantitatively described the ultrastructural timeline of nucleophagy for the first time.
- Non-canonical Role of Dnm1: Revealed the critical role of Dnm1 in nuclear envelope remodeling, expanding its functional scope in cell biology.
- Molecular Mechanism Model: Proposed a molecular mechanism model for nucleophagy, elucidating the collaborative roles of Atg39, Atg11, and Dnm1 in nucleophagy.
Application Value
This study not only holds significant scientific value but also provides potential therapeutic targets for nuclear envelope-related diseases. For example, modulating the activity of Dnm1 may help delay aging or treat diseases associated with nuclear envelope dysfunction. Additionally, the high-resolution microscopy techniques and molecular biology methods used in this study offer new tools and approaches for other cell biology research.
This research provides important insights into the molecular mechanisms of nucleophagy and nuclear envelope remodeling, with broad application prospects.