Institute of Science Tokyo clarifies the mechanism of cell death induced by disruption of nucleophagy

A research team led by Graduate Student Ziyang Li (at the time of the study) and Professor Hitoshi Nakatogawa at the Cell Biology Center, Institute of Integrated Research, Institute of Science Tokyo, has elucidated how the disruption of the pathway of selective degradation of the cell nucleus by autophagy (nucleophagy) leads to cell death. The study was published in Nature Communications.

There are macro and micronucleophagy pathways in yeast cells. In microautophagy, the membranes of lysosomes and vacuoles, which are the compartments where degradation occurs, invaginate and directly sequester and degrade the target molecules. Conversely, degradation targets are sequestered in membrane structures called autophagosomes before they are transported into lysosomes and vacuoles in macroautophagy.

In their previous work in budding yeast, the research team revealed the presence of macronucleophagy, a macroautophagy-mediated mechanism for selective degradation of cell nuclei. The cell nucleus is a large organelle responsible for the storage and replication of genomic DNA and gene expression. In macronucleophagy, part of the cell nucleus is loaded into the autophagosome via the Atg39 protein and degraded in the vacuole.

Macronucleophagy has been known to be important for adaptation to nutrient starvation because Atg39-deficient cells have abnormal cell nuclear morphology under nutrient starvation conditions, and their viability decreases faster than that of wild-type cells. However, it was unknown why the cells have to degrade part of the cell nucleus during nutrient starvation and how the blockage of macronucleophagy leads to abnormal cell nuclear morphology and reduced viability.

Through fluorescence imaging analysis of Atg39-deficient cells exposed to nutrient starvation, the research group found that when macronucleophagy was blocked, large structures containing the contents of the cell nucleus were incorporated into the vacuole. During this process, the vacuolar membrane incorporated the nucleus-derived structures into the vacuole while the vacuolar membrane invaginated. Then, when Nvj1, which is required for micronucleophagy, was deleted, structure uptake was blocked, indicating that the blockage of macronucleophagy leads to an excessive increase in micronucleophagy.

The nuclear membrane protein Nvj1 is degraded by Atg39-dependent macronucleophagy during nutrient starvation, and the accumulation of Nvj1 caused excessive micronucleophagy in the Atg39-deficient cells analyzed in this study. These findings suggest that macronucleophagy prevents hyperactivation of micronucleophagy in normal cells. Furthermore, they observed that the abnormal cell nuclear morphology and reduced viability in Atg39-deficient cells almost completely returned to normal when excessive micronucleophagy was blocked by loss of Nvj1. In other words, it was shown that the blockage of macronucleophagy triggers excessive and fatal micronucleophagy and that suppression of micronucleophagy activity is one of the key roles of macronucleophagy.

In comparison with the nucleus of budding yeast cells (approximately 1.5-2 microns in diameter), the portion degraded by macronucleophagy is smaller (≤0.15 microns). However, the portion degraded by excessive micronucleophagy is very large (>1 micron in diameter in some cases) and contains DNA binding proteins and nucleolar proteins. Therefore, uncontrolled micronucleophagy could lead to cell death because nuclear components essential for survival are incorporated into the vacuole or to the inability of cells to adapt to nutrient starvation because gene expression in the nucleus is affected.

The relationship between excessively enhanced nucleophagy and cell death revealed in this study indicates the importance of controlled, safe nucleophagy and is expected to be useful as fundamental information for understanding related diseases.

Journal Information
Publication: Nature Communications
Title: Macronucleophagy maintains cell viability under nitrogen starvation by modulating micronucleophagy
DOI: 10.1038/s41467-024-55045-9