Study uncovers how genetic mutations linked to childhood neurodegeneration cause essential cellular machine to break down
By combining experiments in baker’s yeast and human cell lines with a generative AI tool, University of Michigan researchers have determined how specific genetic mutations found in children with neurodegenerative diseases disrupt essential cellular processes. Their study, published in the journal Molecular Biology of the Cell, pinpoints the specific defects in a protein machine and could ultimately help in the design of therapies targeting the mutations.
Scientists in the lab of cell biologist Lois Weisman, Ph.D., at the U-M Life Sciences Institute study the intracellular processes that produce a molecule called PI(3,5)P2. Although this signaling lipid normally exists at low levels (so low, in fact, that Weisman’s lab is one of the few in the world that measure it), Weisman and others have demonstrated that minor decreases in this molecule can cause neurodegeneration.
For this lipid to exist at all, three proteins within the cell—called VAC14, PIKfyve and FIG4—must come together to assemble the molecular machine that manufactures PI(3,5)P2. The assembly process brings five VAC14 molecules together to create a star-shaped pentamer, and the other molecules bind to the legs of the star.
Mutations in the gene that encodes VAC14 have been identified in patients with childhood-onset neurodegeneration, as well as some developmental disorders.
“Several investigators had uncovered mutations in VAC14 and showed that they caused severe diseases,” says Weisman, who is a professor of cell and developmental biology at the U-M Medical School and a research professor at the LSI. “But no one knew what the mutations did at the molecular level and how they were causing damage.”
This top-down approach, where we started with known patient mutations and dug into their molecular effects, gave us a new understanding of how the VAC14 complex functions in general and the importance of this complex in cell health.
This pathway is well-conserved in single-celled yeast, the model organism that Weisman’s lab uses to investigate cellular processes underlying neurodegeneration. She recently teamed up with structural biologists to uncover the precise positions of two of these patient mutations.
Using a combination of advanced microscopy and the machine learning system AlphaFold2, the team found that some of the patient mutations occur at the interface between VAC14 proteins. Then, using biochemistry and studies in yeast and human cells, they discovered that the mutations cause the VAC14-PIKfyve-FIG4 complex to fall apart. The researchers also found that cells carrying the VAC14 mutants were defective in the production of the essential PI(3,5)P2 lipid.
“This top-down approach, where we started with known patient mutations and dug into their molecular effects, gave us a new understanding of how the VAC14 complex functions in general and the importance of this complex in cell health,” says Tunahan Uygun, a graduate student in the Weisman lab and one of the study authors. “And the findings raise the possibility that strengthening the VAC14 connections could offer an avenue for targeting these diseases.”
Top Image: Model of the PIKfyve-VAC14-FIG4 complex, based on a previously published structure combined with predictions from AlphaFold2 multimer. Patient mutations in the gene that encodes VAC14 (gray) result in defects in the stability of the complex. Image credit: Tunahan Uygun
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“VAC14 oligomerization is essential for the function of the FAB1/PIKfyve-VAC14-FIG4 complex,” Molecular Biology of the Cell. DOI: 10.1091/mbc.E24-11-0490