New insights into how our cells stay healthy

If we don’t take out the trash regularly, our homes become unpleasant and even dangerous for our health. The same is true of our cells: If excess proteins and strands of genetic material are not removed, the cell and ultimately the entire organism can become ill. For example, scientists suspect a link between Alzheimer’s and mutations that cause defects in cellular waste removal. In addition, tests with mice have shown that suppression of DNA and RNA breakdown can cause severe autoimmune diseases.

However, concrete evidence is lacking: “There is a lot of research showing how genetic information in the form of DNA and RNA is produced in humans. But there is less knowledge about how waste DNA and RNA is removed,” says lab leader Professor Oliver Daumke. at the Max Delbrück Center. To address this, he teamed up with researchers from the University of Kiel to look at waste removal in cells in more detail. Their work focused on an enzyme called PLD3, which is responsible for breaking down the waste. The researchers began by determining its structure using a crystal structure analysis. They were able to identify specific segments that play a key role in the breakdown of RNA and DNA. “This gave us a better understanding of how the waste is broken down and the disease effects of mutations in the PLD3 protein,” says Daumke.

Mutations in the PLD3 gene increase Alzheimer’s risk

PLD3 belongs to a family of protein enzymes that normally break down cellular fats in human cell organelles known as lysosomes. In humans, PLD3 is produced by a gene of the same name.

We have been looking at the PLD3 gene for some time, because it became clear a few years ago that mutations in the gene could be involved in the development of Alzheimer’s.”

Professor Markus Damme of the University of Kiel

“Our work, as well as the work of other researchers, showed that PLD3 actually breaks down DNA and RNA instead of fats,” he says.

“But it wasn’t clear how this was happening,” says Cedric Cappel, a researcher in Damme’s group and co-leader of the paper. “So we decided to look at the protein’s structure more closely – in the hope that we might learn something about its link to Alzheimer’s.” Cappel made some of the protein and sent it to Dr. Yvette Roske, a structural biologist in Daumke’s lab and the paper’s other co-lead author. He succeeded in producing tiny crystals of PLD3. Exposing the crystals to X-rays produced a diffraction pattern that made it possible to reconstruct the protein’s structure. Roske could then image the crystal structure with and without bound RNA and analyze it. “We found that two of these proteins combine to form something called a dimer. We haven’t seen this happen among other enzymes in this family,” says Roske. But why do proteins do this? “It could be because the protein is only stable in one pair,” says Cappel. “On its own, it would probably fall apart.”

Through their work, these two research groups provided the first structural evidence of DNA and RNA cleavage by PLD3. “Now we can get a rough understanding of the reaction mechanism,” says Roske. The researchers also found two regions of the protein that could be key to its function and possibly altered in Alzheimer’s patients – an early indication of a possible disease mechanism.

“The research gave us a map of the protein,” says Cappel. Future studies of PLD3 can use this map to answer questions such as which regions are essential for PLD3 function and what happens when changes are made to these regions. The researchers hope this will lead to a better understanding of the role the protein plays in certain diseases. This knowledge would allow corrective action to be taken.