Scientists capture the cell train that enables transport in cilia

Scientists at St. Jude Children’s Research Hospital deciphered the 3D structure of a key protein complex in cilia that signals appendages found on cells. The structure was recorded with the highest resolution so far. The work serves as the basis for studying diseases of the brain, kidney, skeleton and eyes that are known to affect cilia but have been difficult to study. The results were published today in cell research.

Cilia are hair-like extensions found on almost all mammalian cells that control many signaling processes. The cilium is a type of thin tube that lacks the machinery to synthesize the proteins needed for cell signaling. Therefore, the signaling molecules within the cilia must be brought over from other areas of the cell. Intraflagellar transport complexes, called IFT-A and IFT-B, serve as trains that bring proteins to and from cilia.

For more than a decade scientists have tried to understand the structure of the IFT-A and -B complexes. St. Jude scientists determined the structure of IFT-A with an overall resolution of about 3-4 angstroms, allowing us to visualize these complexes in near-atomic detail.

“Now that we have the high-resolution structure of this ciliary complex, we can map mutations known to cause disease and then design clinical interventions,” said co-corresponding author Ji Sun, Ph.D., St. Jude Department of Structural Biology. “We can tell at the atomic level how these features assemble into very elegant structures in the cilia. We can also use this knowledge to understand how disease mutations disrupt this structure.”

Her work reveals new details that previous attempts were never clear enough to understand. For example, they uncovered previously unknown zinc binding sites in IFT-A. Zinc binding sites are important for a type of protein domain called zinc fingers. Zinc fingers are critical for certain protein-protein interactions, which explains some poorly understood connections within the train complex.

“It was pretty exciting to see the zinc fingers because no one had seen or even predicted zinc binding sites in IFT-A,” Sun said. “Our study was able to show that with confidence. We could say, ‘Hey, there’s zinc, and it’s important for protein-protein interaction, which might also facilitate train assembly.’ Without our high-resolution structural information, we would never have figured that out.”

A molecular ticket to drive

While important, the train is only part of the story. The scientists were able to elucidate the structure of IFT-A in complex with the protein tubby-related protein 3 (TULP3).

“To ride a train, you need a ticket. TULP3 is a ticket to board the IFT-A train,” Sun said. “TULP3 can then identify various acceptable cargoes to be transported on the train. So if you have molecular cargo that can stick to that ticket, it can go on the train. If you disrupt this TULP3 interaction, you will no longer be able to transport certain cargoes because they lack a valid molecular ticket.”

Finding the 3D structure of TULP3 and IFT-A in the complex is a major achievement that will provide insight into how signaling molecules move to and from cilia and how disruption of the interface between the two can cause disease.

Understand ciliary diseases in high resolution

Cilia are important organelles of many species. This high conservation across species tells scientists that cilia are important. Many mutations in ciliary proteins are associated with diseases of various tissues.

However, without structure, it is difficult to explain how changes in proteins cause disease. Therefore, in the last decade, scientists have made many attempts to elucidate the structure of ciliary components. The St. Jude group has managed to fabricate a high-resolution structure of IFT-A using a technique known as single-particle electron cryo-microscopy (cryo-EM).

“The field has waited a long time to see these complexes,” Sun said. “IFT-A is a complex of six proteins. We know that IFT-A mutations affect skeletal development, particularly the ribs, but also structures like the retina. There are many developmental diseases caused by mutations in this complex.”

Combined, the high-resolution structures of IFT-A and TULP3 in the complex can now serve as a basis for studying many developmental diseases involving cilia and help guide the development of new approaches to their alleviation or cure.