What did the researchers at Stanford University discover in their recent study about clearing misfolded proteins from the nucleus?

A new study published in Nature Cell Biology has revealed a previously unknown pathway for clearing misfolded proteins from the nucleus. Misfolded proteins are toxic to cells and can lead to age-related degenerative diseases such as Alzheimer’s, Parkinson’s, and Huntington’s diseases. The discovery of this pathway could be a potential target for therapies to treat such diseases.

To identify this new pathway, researchers at Stanford University used various genetic, imaging, and biochemical techniques to understand how yeast cells dealt with misfolded proteins. The team restricted misfolded proteins to either the nucleus or the cytoplasm and observed their fate through live-cell imaging and super-resolution microscopy.

The researchers found that there is communication between the nucleus and the cytoplasm, and they coordinate to send misfolded proteins to a “garbage dump” site located at the intersection of the nucleus and the vacuole. The vacuole is an organelle filled with enzymes that can degrade proteins, and misfolded proteins in this site are moved inside the vacuole for degradation. The pathway depends on a class of proteins used to create small vesicles for transporting molecules around cells.

The study’s co-lead author, Emily Sontag, explained that this discovery provides a new way to look at neurodegenerative diseases such as Alzheimer’s, Parkinson’s, and Huntington’s diseases, as it ties the clearance of misfolded proteins to a specific family of proteins involved in vesicle traffic biology.

Shared ‘garbage dump’ site for the nucleus and the cytoplasm

Misfolded proteins can be handled by cells through various ways: refolding, elimination, or storage in specific cellular locations. Inclusions, which are clusters of misfolded proteins, can be found in both the cytoplasm and nucleus. These inclusions are sequestered by the cell while it decides whether to refold or degrade the proteins. The researchers discovered that the cell forms small misfolded-protein inclusions in different locations within the nucleus and cytoplasm, and these inclusions migrate towards the boundary between the nucleus and vacuole, which acts as a larger garbage dump. The nuclear and cytoplasmic inclusions then align to face each other, separated by the nuclear envelope. The unexpected communication between the nucleus and cytoplasm in clearing misfolded proteins was surprising to the researchers. The management of misfolded proteins in each compartment is distinct, yet coordinated, with both moving their misfolded proteins to the site where the nuclear envelope meets the vacuolar membrane.

From dump site to degradation: A new pathway

Yeast’s vacuole is similar to the lysosome in mammalian cells and serves as a recycling center for the cell. Misfolded proteins are sequestered into inclusions and transported to the boundary between the nucleus and vacuole, where they are either degraded or stored. The team hypothesized that the inclusions are brought to this specific spot to be sent to the vacuole for degradation. However, the pathway for nuclear inclusions to enter the vacuole was not clear, as they are separated from the vacuole by the nuclear envelope.

To investigate this pathway, the team blocked the proteasome, the other major protein clearance mechanism, and used cryogenic soft X-ray tomography and fluorescence microscopy to create 3D images of the cells containing misfolded protein inclusions. They found that cytoplasmic inclusions entered the vacuole via autophagy, but nuclear inclusions budded straight from the nucleus into the vacuole at the junction of the two membranes. The team also discovered that ESCRT II/III and Vps4 proteins facilitated this budding action, which has not been studied in the context of clearing the nucleus of damaged proteins before. These proteins may have potential as targets for misfolded protein diseases. Finally, using pH-sensitive tags, the team followed the inclusions into the vacuole, providing evidence for this new pathway.

An eye on aging

The experiments conducted by the team were carried out on yeast cells, which are simple to cultivate and have a quick reproductive cycle. The next course of action would be to determine whether the same pathway is used in human cells to clear disease-related proteins.

Another goal is to determine how communication between the nucleus and cytosol occurs along the pathway, as well as how the pathway is affected by the aging process.

Research has indicated that the process for dealing with misfolded proteins slows down with age. As a result, aged cells are unable to eliminate garbage as quickly or efficiently, allowing misfolded proteins to accumulate within the cell.

The researchers demonstrated that nuclear and cytoplasmic quality control pathways communicate through the nuclear envelope, which is damaged by aging and neurodegenerative disease. Numerous progeria mutations, which cause premature aging, distort the nuclear envelope. This research is a significant advancement in our understanding of, and thus treatment of, a wide range of debilitating diseases that affect an increasingly aging population.

Source: Stanford University

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