biostudies-literatureKlossel SDeutsche Forschungsgemeinschaft (DFG)European Research CouncilDeutsche Forschungsgemeinschaft1870-1897https://www.ebi.ac.uk/biostudies/studies/S-EPMC11066047biostudies-literatureUnknown43(9)Yeast vacuoles perform crucial cellular functions as acidic degradative organelles, storage compartments, and signaling hubs. These functions are mediated by important protein complexes, including the vacuolar-type H⁺-ATPase (V-ATPase), responsible for organelle acidification. To gain a more detailed understanding of vacuole function, we performed cross-linking mass spectrometry on isolated vacuoles, detecting many known as well as novel protein-protein interactions. Among these, we identified the uncharacterized TLDc-domain-containing protein Rtc5 as a novel interactor of the V-ATPase. We further analyzed the influence of Rtc5 and of Oxr1, the only other yeast TLDc-domain-containing protein, on V-ATPase function. We find that both Rtc5 and Oxr1 promote the disassembly of the vaThe EMBO journalYeast TLDc domain proteins regulate assembly state and subcellular localization of the V-ATPase.PMC11066047LI 3260/5-1GO 3313/1-1STG 949184949184Zhu YAmado LKlossel SGonzalez Montoro ABisinski DDRuta JLiu FfalseYeast TLDc domain proteins regulate assembly state and subcellular localization of the V-ATPase.Yeast vacuoles perform crucial cellular functions as acidic degradative organelles, storage compartments, and signaling hubs. These functions are mediated by important protein complexes, including the vacuolar-type H⁺-ATPase (V-ATPase), responsible for organelle acidification. To gain a more detailed understanding of vacuole function, we performed cross-linking mass spectrometry on isolated vacuoles, detecting many known as well as novel protein-protein interactions. Among these, we identified the uncharacterized TLDc-domain-containing protein Rtc5 as a novel interactor of the V-ATPase. We further analyzed the influence of Rtc5 and of Oxr1, the only other yeast TLDc-domain-containing protein, on V-ATPase function. We find that both Rtc5 and Oxr1 promote the disassembly of the va2024-01-01T00:00:00Z2024 May2026-06-02T07:02:03.675Z2026-04-15T03:15:35.659ZS-EPMC110660473858961110.1038/s44318-024-00097-2