Jamming cell’s protein disposal shows how system works

CAMBRIDGE, Mass. –Whitehead Institute scientists have determined that a protein known as YOD1 plays a critical role in the disposal of misfolded cellular proteins. The inability of cells to properly remove errant proteins is associated with multiple disorders, including neurodegenerative diseases such as Parkinson’s and Alzheimer’s.

The researchers identified YOD1’s role by blocking its function, a manipulation that halts the elimination of several misfolded model proteins entirely. The finding, reported this month in Molecular Cell, should help bring greater understanding to this vital but complex cellular process.

Whitehead researchers studying human kidney cells found that YOD1 is a crucial part of a ring-shaped protein complex that pulls misfolded proteins from a cellular compartment, called the endoplasmic reticulum (ER), into the surrounding cellular fluid. In the ER, virtually all secreted proteins are assembled and folded into their proper shapes, enabling them to function correctly. Improperly folded proteins can stick together and clog the ER, which can be disastrous.

“This is a life-threatening situation for the cell, so there is a constant quality control going on that gets rid of these misfolded proteins,” says Robert Ernst, a co-first author on the Molecular Cell paper and postdoctoral researcher in the lab of Whitehead Member Hidde Ploegh.

One step in that quality control process is the active removal of misfolded proteins from the ER. As a misfolded protein emerges from the ER through a membrane channel, the cell tags it for destruction. The tags attract a specialized ring of proteins whose job is to reel the misfolded protein from the ER through the center of the ring. However, tagged misfolded proteins are too large to pass through the ring’s center unless, as the researchers discovered, the YOD1 protein perched atop the ring the removes the tags.

“It’s like the improperly folded protein is a huge tree with all sorts of branches,” says Christian Schlieker, a former postdoctoral researcher in Ploegh’s lab and last author of the paper. Schlieker, who is now an Assistant Professor of Molecular Biophysics and Biochemistry at Yale University says, “It’s very difficult to feed that tree into a shredder. And YOD1, we believe, basically trims down those destruction-tag branches to facilitate the shredding process.”

After the stripped misfolded protein passes through the protein ring, the cell seems to tag the protein for destruction again. This time, though, the tags appear to remain in place, and the misfolded protein is shuttled to a membrane-bound sack called the proteasome, whose potent activity degrades proteins to their constituent parts.

During their work, the scientists found that when non-functioning YOD1 is substituted on the ring protein, the misfolded protein removal system completely shuts down at an early stage of removal. The misfit YOD1 is unable to remove the tags from the misfolded protein, jamming the ring protein and leaving the aberrant protein stuck in both the ER channel and in the ring protein.

“You seldom see such a drastic effect – 100 percent shut down of these channels,” says Ernst. “That means we now have an intermediate, which we can employ to learn more about the tagging process itself, but also about the complex events taking place on a misfolded protein on the way to its final destruction by the proteasome.”

Ploegh agrees.

“It’s a great platform to dissect in the test tube how these complicated processes work,” says Ploegh, who is also a professor of biology at MIT. “The most exciting prospect would be that we could use this information to identify the channel through which these misfolded proteins are extracted from the ER, and that would potentially give us a new window on the process.”

This research was funded by the European Molecular Biology Organization (EMBO).

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Hidde Ploegh’s primary affiliation is with Whitehead Institute for Biomedical Research, where his laboratory is located and all his research is conducted. Ploegh is also a professor of biology at Massachusetts Institute of Technology.

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Citation:

Ernst, R., Mueller, B., Ploegh, H. L., & Schlieker, C. (2009). The otubain YOD1 is a deubiquitinating enzyme that associates with p97 to facilitate protein dislocation from the ER. Molecular cell, 36(1), 28-38.