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pH-dependent regulation in SLC38A9.

Xuelang Mu1,2, Ampon Sae Her1, Tamir Gonen1,2,3

  • 1Departments of Biological Chemistry and Physiology, University of California, Los Angeles, CA, USA.

Biorxiv : the Preprint Server for Biology
|November 24, 2025
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Summary
This summary is machine-generated.

The lysosomal transporter SLC38A9

Keywords:
Amino acid transportSLC familyTransceptormTOR complex (mTORC)pH-regulation

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Area of Science:

  • Cellular biology
  • Biochemistry
  • Molecular mechanisms

Background:

  • Cells require strict metabolic regulation for environmental adaptation.
  • The mechanistic target of rapamycin complex 1 (mTORC1) pathway regulates cell growth and metabolism, sensing nutrient availability, particularly amino acids.
  • Lysosomes are crucial for nutrient recycling and maintaining amino acid homeostasis.

Purpose of the Study:

  • To investigate the pH-dependent regulation of the lysosomal amino acid transporter SLC38A9.
  • To identify the specific residues involved in pH sensing and their mechanism of action.
  • To elucidate the structural basis for pH-induced activation of SLC38A9.

Main Methods:

  • Biochemical assays to measure arginine uptake by SLC38A9.
  • Site-directed mutagenesis of the histidine residue His544.
  • Determination of SLC38A9 crystal structures at different pH values.
  • Comparative structural analysis to model pH-induced conformational changes.

Main Results:

  • Arginine transport by SLC38A9 is significantly influenced by pH.
  • The histidine residue His544 was identified as the critical pH sensor, mediating pH-dependent transport.
  • Mutating His544 abolished pH sensitivity without affecting basal transport activity.
  • Structural comparison revealed distinct conformations of SLC38A9 at high and low pH, supporting a model of pH-induced activation.

Conclusions:

  • SLC38A9 activity is regulated by the lysosomal pH.
  • His544 plays a key role in sensing pH changes and modulating transporter function.
  • These findings reveal a novel mechanism of lysosomal transporter regulation and its impact on mTORC1 signaling.