Why does the sodium/proton exchanger NHE9 only function inside cells, and not at the plasma membrane?

Na⁺/H⁺ exchangers (NHEs) play a central role in maintaining pH balance, sodium gradients, and overall cell function. While much is known about plasma membrane isoforms like NHE1, intracellular variants such as NHE9 have remained more elusive. One key question has been why NHE9 is active in endosomes, but silent when expressed at the cell surface.

A recent study published in Nature Communications has now provided compelling structural and functional evidence that the answer lies in lipid regulation.

Using high-resolution cryo-EM, the researchers determined the structure of NHE9 in complex with PI(3,5)P₂, an endosome-specific lipid. They found that this lipid binds at the dimerization interface, stabilizing the functional homodimer. The interaction is mediated by a unique β-hairpin loop between transmembrane helices TM2 and TM3, an architectural feature conserved in endosomal NHE isoforms but absent from plasma membrane variants.

To test function, the team used SSM-based electrophysiology (SURFE²R) to measure Na⁺ transport in proteoliposomes. In the presence of PI(3,5)P₂, NHE9 showed a significant increase in Na⁺ transport, with a roughly four-fold improvement in apparent sodium affinity. In contrast, PI(4,5)P₂, more commonly found in the plasma membrane, had no such effect.

These results were further supported by cell-based assays. NHE9 expressed at the plasma membrane in mammalian cells showed no measurable activity, despite being present in similar amounts as active NHE1. However, when localized within endosomes, where PI(3,5)P₂ is present, the transporter regained full functionality.

This study presents the first structural validation of lipid-mediated dimer stabilization in an intracellular Na⁺/H⁺ exchanger, and suggests a mechanism in which PI(3,5)P₂ acts as a lipid-dependent molecular switch, activating NHE9 only upon proper endosomal localization.

Beyond advancing our understanding of transporter regulation, these findings may have implications for diseases linked to NHE9 dysfunction. Mutations in the SLC9A9 gene have been associated with neurological conditions such as autism, ADHD, and epilepsy, pointing to the relevance of this regulatory mechanism in human health.

Find the full article here:
PIP2-mediated oligomerization of the endosomal sodium/proton exchanger NHE9

Explore SSM-based electrophysiology with SURFE²R here:
https://www.nanion.de/products/surfe2r-n1/