Researchers discover how nature repurposes ammonium transporters as receptors

Unlike other proteins that transport water or potassium, ammonium transporters (Amts) are special because they can tell ammonium apart from potassium and water. This special ability helped them evolve to become ammonium sensors. Exploring ammonium sensing in biological systems provides insights in to essential processes, such as regulation of nutrient uptake or cellular signaling.

Now a team of scientists from the University of Freiburg has characterised a new membrane protein, called Sd-Amt1, that allows microorganisms to repurpose ammonium transporters (Amts) as receptors.

The researchers looked at the structure of this receptor both with and without ammonium attached, at very high detail (down to 1.7 and 1.9 Ångstroms). This helped them understand how the receptor switches between "ON" (with ammonium) and "OFF" (without ammonium) states. The newly discovered protein uses ammonium cations as extracellular signals to increase the cytoplasmic level of the secondary messenger cyclic-di-GMP. It consists of a membrane-integral ammonium receptor domain linked to a cytoplasmic diguanylate cyclase transducer module.

Synchrotron, Cryo-EM and Alphafold

The research work has included synchrotron structural biology studies at the ESRF and SLS in Switzerland and Cryo-EM at the ESRF. “Combining single particle cryo-EM with protein crystallography, AlphaFold predictions, and functional assays allowed us to reach a comprehensive understanding of Sd-Amt1 in molecular level”, explains Susana Andrade, Professor at the University of Freiburg and corresponding author of the article. And she adds: “Such an integrative approach feeds from the ability of cryo-EM to visualise proteins in near-native conditions, the detailed high-resolution insights from protein crystallography and the predictive modeling aspects of AlphaFold with experimental validation, resulting in a detailed and robust characterisation of protein mechanisms”. 

The team discovered the molecular details of ammonium-triggered signal binding, receptor activation and transducer modulation. They also showed the extent to which the signal binding motif is conserved between prokaryotic and eukaryotic organisms, providing a signature motif to identify other ammonium receptors.

Reference:

Pflüger, T. et al., Science Advances. DOI: 10.1126/sciadv.adm9441

Top image: Membrane protein Sd-Amt1 in the bacterium Shewanella denitrificans. Credits: Susana Andrade