Ordered deployment of distinct ciliary beating machines in growing axonemes of vertebrate multiciliated cells

An amino acid-resolution interactome for motile cilia identifies the structure and function of ciliopathy protein complexes

Motile cilia are ancient, evolutionarily conserved organelles whose dysfunction underlies motile ciliopathies, a broad class of human diseases. Motile cilia contain a myriad of different proteins that assemble into an array of distinct machines, and understanding the interactions and functional hierarchies among them presents an important challenge. Here, we defined the protein interactome of motile axonemes using cross-linking mass spectrometry in Tetrahymena thermophila. From over 19,000 cross-links, we identified over 4,700 unique amino acid interactions among over 1,100 distinct proteins, providing both macromolecular and atomic-scale insights into diverse ciliary machines, including the intraflagellar transport system, axonemal dynein arms, radial spokes, the 96-nm ruler, and microtubule inner proteins. Guided by this dataset, we used vertebrate multiciliated cells to reveal functional interactions among several poorly defined human ciliopathy proteins. This dataset provides a resource for studying the biology of an ancient organelle and the molecular etiology of human genetic disease.

Molecular organization of the distal tip of vertebrate motile cilia

The beating of cilia on multi-ciliated cells (MCCs) is essential for normal development and homeostasis in animals. Unlike basal bodies or axonemes, the distal tips of MCC cilia remain poorly defined. Here, we characterize the molecular organization of the distal tip of vertebrate MCC cilia, revealing two distinct domains occupied by distinct protein constituents. Using frog, mouse, and human MCCs, we find that two largely uncharacterized proteins, Ccdc78 and Ccdc33 occupy a specialized region at the extreme distal tip, and these are required for the normal organization of other tip proteins, including Spef1, Cep104, and Eb3. Ccdc78 and Cccdc33 are also independently required for normal length regulation of MCC cilia. Mechanistically, Ccdc78 and Ccdc33 display robust microtubule-bundling activity both in vivo and in vitro . Thus, we reveal that two previously undefined proteins form a key module for organizing and stabilizing the distal tip of motile cilia in vertebrate MCC. We propose that these proteins represent potential disease loci for motile ciliopathies.

Label-free proteomic comparison reveals ciliary and nonciliary phenotypes of IFT-A mutants

DIFFRAC is a powerful method for systematically comparing proteome content and organization between samples in a high-throughput manner. By subjecting control and experimental protein extracts to native chromatography and quantifying the contents of each fraction using mass spectrometry, it enables the quantitative detection of alterations to protein complexes and abundances. Here, we applied DIFFRAC to investigate the consequences of genetic loss of Ift122, a subunit of the intraflagellar transport-A (IFT-A) protein complex that plays a vital role in the formation and function of cilia and flagella, on the proteome of Tetrahymena thermophila. A single DIFFRAC experiment was sufficient to detect changes in protein behavior that mirrored known effects of IFT-A loss and revealed new biology. We uncovered several novel IFT-A-regulated proteins, which we validated through live imaging in Xenopus multiciliated cells, shedding new light on both the ciliary and non-ciliary functions of IFT-A. Our findings underscore the robustness of DIFFRAC for revealing proteomic changes in response to genetic or biochemical perturbation.