Human V-ATPase function is positively and negatively regulated by TLDc proteins

Knockout of the V-ATPase interacting protein Tldc2 in B-type kidney intercalated cells impairs urine alkalinization

Intercalated cells (ICs) are acid-base regulatory cells in the kidney collecting duct that excrete either acid or base into the urine in response to systemic cues. A-ICs deliver protons into the tubule lumen via an apical proton pump (V-ATPase) and reabsorb base (bicarbonate) using the anion exchanger 1 (AE1) anion exchanger. B-ICs function in the opposite direction. They have basolateral V-ATPase and secrete bicarbonate into the lumen via the anion exchange protein pendrin. The function of a third IC subtype: the non-A, non-B IC, which has apical pendrin and apical V-ATPase, is less well understood. We previously reported that members of the TLDc protein family interact with the V-ATPase and may regulate its function. TLDc proteins exhibit a distinct expression pattern in the kidney with RNAseq showing high, differential expression of Tldc2 in B-ICs. Here, we show by RNAscope imaging that Tldc2 is indeed expressed in B-ICs but also in some non-A, non-B ICs. Using Tldc2 knockout (Tldc2-/-) mice, we found that males and females had significantly lower urine pH than wild-type littermates and their ability to increase urine pH in response to a bicarbonate load was impaired. In addition, Tldc2-/- males developed hyperbicarbonatemia. Tldc2-/- kidneys contained fewer B-ICs than wild-type mice, but they were replaced by more non-A, non-B ICs; the number of A-ICs was unchanged. Finally, there was decreased basolateral accumulation of V-ATPase in Tldc2-/- B-ICs. These findings suggest that Tldc2 is a novel gene involved in renal acid-base regulation and in addition, may serve as a differentiation marker for B-ICs.NEW & NOTEWORTHY Acid-base balance in the body is constantly changing but must be tightly controlled to be compatible with life. The kidney contains specialized cells that can excrete excess acid or base (bicarbonate) into the urine to maintain normal blood pH. The key protein involved in this process is called the V-ATPase. Here, we report that a novel V-ATPase interacting protein Tldc2 is critical for kidney bicarbonate secretion and is, therefore, a previously unrecognized acid-base regulatory gene.

V-ATPase Disassembly at the Yeast Lysosome-Like Vacuole Is a Phenotypic Driver of Lysosome Dysfunction in Replicative Aging

Declines in lysosomal acidification and function with aging are observed in organisms ranging from yeast to humans. V-ATPases play a central role in organelle acidification, and V-ATPase activity is regulated by reversible disassembly in many different settings. Using the yeast Saccharomyces cerevisiae as a replicative aging model, we demonstrate that V-ATPases disassemble into their V1 and V0 subcomplexes in aging cells, with release of V1 subunit C (Vma5) from the lysosome-like vacuole into the cytosol. Disassembly is observed after > 5 cell divisions and results in overall vacuole alkalinization. Caloric restriction, an established mechanism for reversing many age-related outcomes, prevents V-ATPase disassembly in older cells and preserves vacuolar pH homeostasis. Reversible disassembly is controlled in part by the activity of two opposing and conserved factors: the Regulator of Acidification of Vacuoles and Endosomes (RAVE) complex and Oxr1. The RAVE complex promotes V-ATPase assembly and a rav1∆ mutant shortens replicative lifespan; Oxr1 promotes disassembly and an oxr1∆ mutation extends the lifespan. Importantly, the level of Rav2, a subunit of the RAVE complex, declines in aged cells, and Rav2 overexpression delays V-ATPase disassembly with age. These data indicate that reduced V-ATPase assembly contributes to the loss of lysosomal acidification with age, which affects replicative lifespan.

EndoMAP.v1, a Structural Protein Complex Landscape of Human Endosomes

Early/sorting endosomes are dynamic organelles that play key roles in proteome control by triaging plasma membrane proteins for either recycling or degradation in the lysosome1,2,3. These events are coordinated by numerous transiently-associated regulatory complexes and integral membrane components that contribute to organelle identity during endosome maturation4. While a subset of the several hundred protein components and cargoes known to associate with endosomes have been studied at the biochemical and/or structural level, interaction partners and higher order molecular assemblies for many endosomal components remain unknown. Here, we combine cross-linking and native gel mass spectrometry5-8 of purified early endosomes with AlphaFold9,10 and computational analysis to create a systematic human endosomal structural interactome. We present dozens of structural models for endosomal protein pairs and higher order assemblies supported by experimental cross-links from their native subcellular context, suggesting structural mechanisms for previously reported regulatory processes. Using induced neurons, we validate two candidate complexes whose interactions are supported by crosslinks and structural predictions: TMEM230 as a subunit of ATP8/11 lipid flippases11 and TMEM9/9B as subunits of CLCN3/4/5 chloride-proton antiporters12. This resource and its accompanying structural network viewer provide an experimental framework for understanding organellar structural interactomes and large-scale validation of structural predictions.

TBC1D24 interacts with the v-ATPase and regulates intraorganellar pH in neurons

The vacuolar ATPase (v-ATPase) is essential for acidification of intracellular organelles, including synaptic vesicles. Its activity is controlled by cycles of association and dissociation of the ATP hydrolysis (V1) and proton transport (V0) multi-protein subunits. Mutations in genes coding for both v-ATPase subunits and TBC1D24 cause neurodevelopmental disorders with overlapping syndromes; therefore, it is important to investigate their potentially interrelated functions. Here, we reveal that TBC1D24 interacts with the v-ATPase in the brain. Using a constitutive Tbc1d24 knockout mouse model, we observed accumulation of lysosomes and non-degraded lipid materials in neuronal tissue. In Tbc1d24 knockout neurons, we detected V1 mis-localization with increased pH at endo-lysosomal compartments and autophagy impairment. Furthermore, synaptic vesicles endocytosis and reacidification were impaired. Thus, we demonstrate that TBC1D24 is a positive regulator of v-ATPase activity in neurons suggesting that alteration of pH homeostasis could underlie disorders associated with TBC1D24 and the v-ATPase.

Monoclonal nanobodies alter the activity and assembly of the yeast vacuolar H+-ATPase

The vacuolar ATPase (V-ATPase; V1Vo) is a multi-subunit rotary nanomotor proton pump that acidifies organelles in virtually all eukaryotic cells, and extracellular spaces in some specialized tissues of higher organisms. Evidence suggests that metastatic breast cancers mislocalize V-ATPase to the plasma membrane to promote cell survival and facilitate metastasis, making the V-ATPase a potential drug target. We have generated a library of camelid single-domain antibodies (Nanobodies; Nbs) against lipid-nanodisc reconstituted yeast V-ATPase Vo proton channel subcomplex. Here, we present an in-depth characterization of three anti-Vo Nbs using biochemical and biophysical in vitro experiments. We find that the Nbs bind Vo with high affinity, with one Nb inhibiting holoenzyme activity and another one preventing enzyme assembly. Using cryoEM, we find that two of the Nbs bind the c subunit ring of the Vo on the lumen side of the complex. Additionally, we show that one of the Nbs raised against yeast Vo can pull down human V-ATPase (HsV1Vo). Our research demonstrates Nb versatility to target and modulate the activity of the V-ATPase, and highlights the potential for future therapeutic Nb development.

V-ATPase Dysfunction in the Brain: Genetic Insights and Therapeutic Opportunities

Vacuolar-type ATPase (v-ATPase) is a multimeric protein complex that regulates H+ transport across membranes and intra-cellular organelle acidification. Catabolic processes, such as endocytic degradation and autophagy, strictly rely on v-ATPase-dependent luminal acidification in lysosomes. The v-ATPase complex is expressed at high levels in the brain and its impairment triggers neuronal dysfunction and neurodegeneration. Due to their post-mitotic nature and highly specialized function and morphology, neurons display a unique vulnerability to lysosomal dyshomeostasis. Alterations in genes encoding subunits composing v-ATPase or v-ATPase-related proteins impair brain development and synaptic function in animal models and underlie genetic diseases in humans, such as encephalopathies, epilepsy, as well as neurodevelopmental, and degenerative disorders. This review presents the genetic and functional evidence linking v-ATPase subunits and accessory proteins to various brain disorders, from early-onset developmental epileptic encephalopathy to neurodegenerative diseases. We highlight the latest emerging therapeutic strategies aimed at mitigating lysosomal defects associated with v-ATPase dysfunction.

The merger of two major families of proteins that regulate cellular processes

In this issue of Structure, Oot and Wilkens1 present new mechanistic insights to finally merge the function of V-ATPase and TLDc domain proteins. They show that TLDc proteins directly affect V-ATPase activity and assembly, expanding our understanding of how V-ATPase and TLDc proteins exert a plethora of biological functions.