Probing the interaction between the WDR41 7CD loop of the C9ORF72 complex and purified PQLC2

The lysosomal cationic amino acid transceptor PQLC2 integrates transport with receptor-like signaling roles by recruiting the C9ORF72/SMCR8/WDR41 (CSW) complex in response to cellular cationic amino acid depletion. CSW recruitment depends on the interaction of PQLC2 with a disordered loop (7CD loop) extending from the WDR41 {beta}-propeller. Defining the molecular basis of this interaction is therefore essential for understanding how PQLC2 connects cellular amino acid availability to downstream signaling. Here, we used site-directed electron paramagnetic resonance (EPR) spectroscopy to characterize the interaction between purified PQLC2 and a synthetic WDR41 7CD loop peptide containing a site-specific nitroxide spin label. Using a consensus mutagenesis strategy, we stabilized detergent-purified PQLC2 and found that it assembles as a homotrimer, similar to other PQ-loop transporters. EPR experiments demonstrated the direct and specific association of the 7CD loop with PQLC2, and highlighted the key role of the the central region of the 7CD loop to establish this interaction via conserved aromatic residues. Spin labels introduced at different positions further provided local structural and dynamic information of the 7CD loop upon PQLC2 binding. The data supports a model in which the central region of the loop is anchored within the cytosolic cavity of PQLC2, whereas the flanking regions, which are dispensable for binding, retain substantial conformational flexibility. Together, we provide a direct biochemical evidence for PQLC2/WDR41 7CD loop recognition, a step forward towards understanding the transceptor mechanism of PQLC2.