Dr. Li-Lin Du’s laboratory discovers a factor required for ER-phagy and nucleophagy

On November 8, 2023, Dr. Li-Lin Du’s laboratory published a research paper entitled "The ortholog of human REEP1-4 is required for autophagosomal enclosure of ER-phagy/nucleophagy cargos in fission yeast" in PLOS Biology. In this study, the authors identified a protein named Yep1 that is essential for ER-phagy and nucleophagy in the model organism the fission yeast Schizosaccharomyces pombe. Yep1 plays a critical role in the autophagosomal enclosure of cargos during ER-phagy and nucleophagy.

The endoplasmic reticulum (ER) is an important and complex organelle in eukaryotic cells. The nuclear envelope is connected to the ER. Under conditions of nutrient starvation or ER stress, cells degrade the ER through a selective autophagy process called ER-phagy. During ER-phagy, portions of the ER are first sequestered within autophagosomes. This process is mediated by selective autophagy receptors. The autophagosomes then fuse with lysosomes, enabling the engulfed ER fragments to be broken down through lysosomal degradation. The nuclear envelope is also degraded by selective autophagy, and part of the nucleoplasm is enclosed within autophagosomes during autophagosomal enclosure of the nuclear envelope. This selective autophagy process is called nucleophagy. The molecular mechanisms underlying ER-phagy and nucleophagy are not yet fully understood.

In this study, the authors performed a genetic screen based on high-content microscopy analysis of chemically mutagenized mutants and identified a mutant that cannot undergo ER-phagy. They then used genetic linkage analysis based on high-throughput sequencing to locate the mutation causing the phenotype to the yep1 gene. Analysis of a yep1 knockout mutant revealed that the absence of Yep1 does not affect the binding between the ER-phagy/nucleophagy receptor Epr1 and core autophagic protein Atg8, but prevents ER-phagy/nucleophagy cargos from being successfully enclosed within autophagosomes, leading to their accumulation in the cytoplasm (Figure 1). The authors found that the inner membranes of nucleophagy cargos accumulated in the cytoplasm were no longer connected to the ER/nuclear envelope, but the outer membranes were still connected to the ER/nuclear envelope. The authors speculated that the defect in ER-phagy and nuclear autophagy could possibly be due to either of the two following reasons: firstly, Yep1 may be involved in the process of separating the outer membrane of the cargo from the ER/nuclear envelope, i.e., in the absence of Yep1, failure to separate the outer membrane from the ER/nuclear membrane leads to failure of the cargo to be enclosed within autophagosomes; secondly, Yep1 may participate in the process of cargo packaging on autophagosome precursors.

Further analysis revealed that Yep1 has ER-shaping ability, which is important for its function in ER-phagy. Additionally, the authors found that Yep1's function in ER-phagy depends on its self-interaction and its C-terminal amphipathic helices.

Yep1 belongs to the REEP protein family, which is conserved across eukaryotes. This protein family consists of two subfamilies: REEP1-4 subfamily and REEP5-6 subfamily. Yep1 is a REEP1-4 subfamily protein. The authors found that human REEP1-4 subfamily proteins can replace Yep1 to perform ER-phagy function in fission yeast, but human REEP5-6 subfamily proteins cannot replace Yep1. The authors showed that budding yeast ER-phagy factor Atg40 is also a member of REEP1-4 subfamily and can replace Yep1 to perform ER-phagy function in fission yeast. These findings suggest that REEP1-4 subfamily proteins may be involved in ER-phagy in eukaryotes generally.

Chen-Xi Zou is the first author of this paper. Dr. Li-Lin Du is the corresponding author. Other contributors include Zhu-Hui Ma, Zhao-Di Jiang, Zhao-Qian Pan, Dan-Dan Xu, Fang Suo, Guang-Can Shao, and Meng-Qiu Dong. The study was conducted at the National Institute of Biological Sciences, Beijing and was supported by the Ministry of Science and Technology, the Beijing Municipal Government, and Tsinghua University.

Link to the paper: https://doi.org/10.1371/journal.pbio.3002372

Figure 1. Cytoplasmic accumulation of ER-phagy/nucleophagy cargos revealed by electron microscopy analysis.