Regulation of V-ATPase Activity and Organelle pH by Phosphatidylinositol Phosphate Lipids

Abstract

Luminal pH and the distinctive distribution of phosphatidylinositol phosphate (PIP) lipids are central identifying features of organelles in all eukaryotic cells that are also critical for organelle function. V-ATPases are conserved proton pumps that populate and acidify multiple organelles of the secretory and the endocytic pathway. Complete loss of V-ATPase activity causes embryonic lethality in higher animals and conditional lethality in yeast, while partial loss of V-ATPase function is associated with multiple disease states. On the other hand, many cancer cells increase their virulence by upregulating V-ATPase expression and activity. The pH of individual organelles is tightly controlled and essential for function, but the mechanisms for compartment-specific pH regulation are not completely understood. There is substantial evidence indicating that the PIP content of membranes influences organelle pH. We present recent evidence that PIPs interact directly with subunit isoforms of the V-ATPase to dictate localization of V-ATPase subpopulations and participate in their regulation. In yeast cells, which have only one set of organelle-specific V-ATPase subunit isoforms, the Golgi-enriched lipid PI(4)P binds to the cytosolic domain of the Golgi-enriched a-subunit isoform Stv1, and loss of PI(4)P binding results in mislocalization of Stv1-containing V-ATPases from the Golgi to the vacuole/lysosome. In contrast, levels of the vacuole/lysosome-enriched signaling lipid PI(3,5)P 2 affect assembly and activity of V-ATPases containing the Vph1 a-subunit isoform. Mutations in the Vph1 isoform that disrupt the lipid interaction increase sensitivity to stress. These studies have decoded "zip codes" for PIP lipids in the cytosolic N-terminal domain of the a-subunit isoforms of the yeast V-ATPase, and similar interactions between PIP lipids and the V-ATPase subunit isoforms are emerging in higher eukaryotes. In addition to direct effects on the V-ATPase, PIP lipids are also likely to affect organelle pH indirectly, through interactions with other membrane transporters. We discuss direct and indirect effects of PIP lipids on organelle pH, and the functional consequences of the interplay between PIP lipid content and organelle pH.

ApoE-Isoform-Dependent SARS-CoV-2 Neurotropism and Cellular Response

“…Among the host genes examined, ACTR2 (endosomal entry), ATP6AP2 (spike protein cleavage, endosomal acidification and processing), ERMP1 (ER), and CHST14 (Golgi) showed higher expression levels in ApoE4 astrocytes than that in ApoE3 astrocytes ( Figures 3 E and 3F). Of the differentially expressed host factors, ACTR2 is an actin cytoskeleton-associated protein that is involved in endosomal entry ( Daniloski et al., 2020 ), while ATP6AP2 is a subunit of the vacuolar-ATPase proton pump important for endosomal acidification and processing ( Banerjee and Kane, 2020 ). Indeed, increased number and size of early endosomes have been detected in ApoE4 cells and brains compared to their ApoE3 counterparts ( Cataldo et al., 2000 ; Lin et al., 2018 ).…”

DRAM1 requires PI(3,5)P2generation by PIKfyve to deliver vesicles and their cargo to endolysosomes

“…The identity of endolysosomal vesicles is in part determined by the presence of phosphoinositide (PI) lipids in their membrane that serve as docking sites for effector proteins (Hammond et al, 2012;Heo et al, 2006;Strahl and Thorner, 2007). PIs can be phosphorylated and dephosphorylated on the hydroxyl groups at the three, four, and five positions of their inositol rings by a range of kinases and phosphatases, generating a total of 7 different PIs in animals (Banerjee and Kane, 2020). Typically, early endosomes are defined by the presence of PI(3)P in their membrane, which is converted into PI(3,5)P 2 by the lipid kinase PIKfyve (Fab1p in yeast) during maturation into late endosomes (Wallroth and Haucke, 2018).…”

Faculty Opinions recommendation of Identification of Required Host Factors for SARS-CoV-2 Infection in Human Cells.

“…, and TOR1AIP1), endosome recycling (4 members of the endosomal protein sorting Retromer complex: VPS26A, VPS29, VPS35, and SNX27; 4 members of the endosomal trafficking Commander complex: COMMD2, COMMD3, COMMD3-BMI1, and COMMD4; and 3 members of the PI3K pathway: PIK3C3/VPS34, WDR81, and ACP5), ER-Golgi trafficking (DPM3, ERMP1, PPID, and CHST14), and transcriptional modulators (SLTM and SPEN). A consistent theme among the enriched complexes is endosome function and regulation (V-ATPase proton pump, Retromer, Commander, class 3 PI3Ks) (Banerjee and Kane, 2020;Mallam and Marcotte, 2017;McNally and Cullen, 2018). Gene set enrichment analysis on the full ranked list of genes identified significantly enriched Gene Ontology (GO) categories for endosome processing, transport, and acidification and categories related to cytokinesis and virion attachment (false discovery rate [FDR] q < 0.1) (Figures 3B and S2A-S2D; Table S2; Subramanian et al, 2005).…”

“…genes that were highly enriched in all 3 viral pathogen screens ( Figure S2E). This group included subunits of the vacuolar-ATPase proton pump, a well-known family of genes essential for acidification and endosomal processing (Banerjee and Kane, 2020).…”