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Structure, function and regulation of ammonium transport proteins of the Mep-Amt-Rh superfamily in the yeast Saccharomyces cerevisiae

par Soto Diaz, Silvia
Président du jury Vanhamme, Luc
Promoteur Marini, Anna Maria
Co-Promoteur Boeckstaens, Mélanie
Publication Non publié, 2020-10-28

Thèse de doctorat

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Résumé :

While ammonium is an excellent nitrogen source for microorganisms and plants, it is known as acytotoxic metabolite and for its critical role in acid/base homeostasis in animals. Ammonium transportinside the cells is ensured by proteins of the Mep-Amt-Rh superfamily, which are conserved frombacteria to humans.The main objective of the thesis is to refine the understanding of the regulation of the three ammoniumtransport proteins Mep1, Mep2 and Mep3 from Saccharomyces cerevisiae. The three Mep proteins areregulated by the Npr1 kinase and the conserved TORC1 signaling pathway. While the activity of Mep2is regulated by phosphorylation of the C-terminal 457 serine, the activity of Mep1 and Mep3 is inhibitedby the factor Amu1 / Par32. In the presence of a poor nitrogen source, Npr1 induces phosphorylation ofAmu1 which appears mainly cytosolic and, Mep1 and Mep3 are active. On the other hand, in thepresence of a good nitrogen source, the activity of TORC1 induces the inhibition of Npr1 and thereforethe dephosphorylation of Amu1 which accumulates at the cell surface and inactivates Mep1 and Mep3.In order to further study the regulation of Mep1 / 3, a genetic screen was performed to isolate suppressorsrecovering Mep1-dependent ammonium transport in the absence of Npr1. Several mutations, insertionsand deletions have been identified in the MEP1 and AMU1 genes allowing Mep1 to be activeindependently of Npr1. This work shows that all the point mutations in Mep1 delimit an area at theinterface between the hydrophobic body of Mep1 and the cytosol, and that part of the C-terminus (CTR)is required for optimal activity of Mep1 but appears dispensable for regulation by Amu1 and Npr1. Thegenetic screen also shows that the last 15 amino acids of Amu1 are required to inactivate Mep1. Finally,the isolation of suppressors showing no mutation in MEP1 and AMU1 could reveal new factors involvedin the control of Mep1.The results indicate that Mep1 is inactivated in the presence of glutamine, a good source of nitrogen,and that this inactivation requires Amu1. The glutamine-dependent inactivation of Mep2 was alsostudied in this manuscript. Mass spectrometry analysis revealed putative phosphorylation sites in CTRspecific to the presence or absence of glutamine.This work also addressed the role of Amu1 in the reactivation function of TORC1 after treatment withrapamycin, in particular by confirming that it requires the function of Mep1/3. The study leads to thehypothesis that the transport mechanism specific to Mep1 and Mep3 and different from Mep2 isinvolved in this function.Finally, in order to better understand the mechanisms of regulation and transport of Mep-Amt-Rhproteins, the experimental determination of the three-dimensional structure of different variants ofMep2, in open or closed conformation, and of Mep1 was undertaken. Throughout this work, thecharacterized Mep1 or Mep2 variants were analyzed in silico by using the available three-dimensionalstructures.