The primary cilium is a microtubule-based, antenna-like organelle present on nearly every cell in the human body. It plays a crucial role in sensing and transducing environmental signals to guide cell behaviour during development. Disruption of ciliary trafficking pathways leads to a range of severe developmental and degenerative diseases, collectively known as ciliopathies.
At the heart of ciliary assembly and functions is a transport system that traffics building blocks and signalling molecules into and out of the cilium. It employs multi-megadalton ‘IFT trains’ that transport cargoes along the ciliary microtubules under the power of kinesin-2 and dynein-2 motor proteins.
A remarkable feature of IFT is that trains reverse direction specifically at the ciliary tip, switching from kinesin- to dynein-driven motility, making IFT an excellent model for studying regulated directional transport [1,2]. We recently determined the cryo-EM structures of dynein-2 [3] and the IFT-A [1] complex, used CRISPR/Cas9 genome editing [4] to dissect their roles, and obtained molecular insight into how kinesin-2 is inhibited [5]. Together, these advances provide a foundation for determining how IFT train directionality is regulated.
The central goal of this PhD project is to determine the molecular mechanisms by which IFT trains change direction precisely at the ciliary tip.
To achieve this, the project will combine state-of-the-art techniques, including:
- Cryo-electron microscopy (cryo-EM) and cryo-electron tomography (cryo-ET)
- Live-cell fluorescence microscopy
- CRISPR-based genetic tools
- Interaction screening using AlphaFold
By integrating structural, cell and computational biology approaches, this project aims to reveal the molecular logic underlying one of the cell’s most precisely regulated transport systems, with the potential to uncover fundamental mechanisms relevant to human health and disease.
Funding Notes
4 Year DPhil Prize Studentships cover full University fees, a tax free enhanced stipend of ~£24,305 pa, and up to £5,300 pa for research costs and travel. The competition is open to applicants from all countries. See the institution website for full details and to apply.
References
IFT-A Structure Reveals Carriages for Membrane Protein Transport into Cilia (2022) Hesketh SJ, Mukhopadhyay AG, Nakamura D, Toropova K, Roberts AJ.
Cell, 185(26):4971-4985
[2] Intraflagellar Transport Trains and Motors (2020) Webb S, Mukhopadhyay AG, Roberts AJ.
Seminars in Cell & Developmental Biology, 107:82-90
[3] Structure of the Dynein-2 Complex and its Assembly with Intraflagellar Transport Trains (2019) Toropova K, Zalyte R, Mukhopadhyay AG, Mladenov M, Carter AP, Roberts AJ.
Nature Structural & Molecular Biology, 26(9):823-829
[4] Structure and Tethering Mechanism of Dynein-2 Intermediate chains in Intraflagellar Transport (2024) Mukhopadhyay AG, Toropova K, Daly L, Wells JN, Vuolo L, Mladenov M, Seda M, Jenkins D, Stephens DJ, Roberts AJ.
EMBO J 43(7):1257-1272
[5] Regulation of Kinesin-2 Motility by its β-hairpin Motif (2025) Webb S, Toropova K, Mukhopadhyay AG, Nofal SD, Roberts AJ.
Nature Structural & Molecular Biology 32(8):1989-1998
