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1. Model-based inference of a dual role for HOPS in regulating guard cell vacuole fusion

   https://doi.org/10.1093/insilicoplants/diae015  

   Hodgens, Charles; Flaherty, D T; Pullen, Anne-Marie; Khan, Imran; English, Nolan J; Gillan, Lydia; Rojas-Pierce, Marcela; Akpa, Belinda S (August 2024, in silico Plants)

   Zhu, Xin-Guang (Ed.)

   Abstract Guard cell movements depend, in part, on the remodelling of vacuoles from a highly fragmented state to a fused morphology during stomata opening. Indeed, full opening of plant stomata requires vacuole fusion to occur. Fusion of vacuole membranes is a highly conserved process in eukaryotes, with key roles played by two multi-subunit complexes: HOPS (homotypic fusion and vacuolar protein sorting) and SNARE (soluble NSF attachment protein receptor). HOPS is a vacuole tethering factor that is thought to chaperone SNAREs from apposing vacuole membranes into a fusion-competent complex capable of rearranging membranes. In plants, recruitment of HOPS subunits to the tonoplast has been shown to require the presence of the phosphoinositide phosphatidylinositol 3-phosphate. However, chemically depleting this lipid induces vacuole fusion. To resolve this counter-intuitive observation regarding the role of HOPS in regulating plant vacuole morphology, we defined a quantitative model of vacuole fusion dynamics and used it to generate testable predictions about HOPS-SNARE interactions. We derived our model by using simulation-based inference to integrate prior knowledge about molecular interactions with limited, qualitative observations of emergent vacuole phenotypes. By constraining the model parameters to yield the emergent outcomes observed for stoma opening—as induced by two distinct chemical treatments—we predicted a dual role for HOPS and identified a stalled form of the SNARE complex that differs from phenomena reported in yeast. We predict that HOPS has contradictory actions at different points in the fusion signalling pathway, promoting the formation of SNARE complexes, but limiting their activity. 

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2. Regulation of Vacuole Fusion in Stomata by Dephosphorylation of the HOPS subunit VPS39

   https://doi.org/10.1101/2025.10.02.680005  

   Pullen, Anne-Marie; Billings, Grant; Hodgens, Charles; White, Gisele; Akpa, Belinda S; Rojas-Pierce, Marcela (October 2025, bioRxiv)

   ABSTRACT Understanding how plants regulate water loss is important for improving crop productivity. Tight control of stomatal opening and closing is essential for the uptake of CO₂while mitigating water vapor loss. The opening of stomata is regulated in part by homotypic vacuole fusion, which is mediated by conservedhomotypic vacuoleproteinsorting (HOPS) and vacuolar SNARE (soluble N-ethylmaleimide sensitive factor attachment protein receptors) complexes. HOPS tethers apposing vacuole membranes and promotes the formation oftrans-SNARE complexes to mediate fusion. In yeast, HOPS dissociates from the assembled SNARE complex to complete vacuole fusion, but little is known about this process in plants. HOPS-specific subunits VACUOLE PROTEIN SORTING39 (VPS39) and VPS41 are required for homotypic plant vacuole fusion, and a computational model predicted that post-translational modifications of HOPS may be needed for plant stomatal vacuole fusion. Here, we characterized a viable T-DNA insertion allele ofVPS39which demonstrated a critical role of VPS39 in stomatal vacuole fusion. We found that VPS39 has increased levels of phosphorylation when stomata are closed versus open, and that VPS39 function in stomata and embryonic development requires dynamic changes in phosphorylation. Our data are consistent with VPS39 phosphorylation altering vacuole dynamics in response to environmental cues, similar to well-established phosphorylation cascades that regulate ion transport during stomatal opening. SIGNIFICANCE STATEMENTVacuole fusion is important for stomata opening but how it is regulated in response of stomata opening signals is not characterized. This research demonstrated the role of the HOPS complex in vacuole fusion in stomata, and it identified phosphorylation sites in the HOPS subunit VPS39 that are critical for vacuole fusion. One Ser residue was enriched in closed stomata and represents a putative site for control of vacuole fusion downstream of stomata opening signals. 

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3. Plant Cell Vacuoles: Staining and Fluorescent Probes

   Stefano, Giovanni; Renna, Luciana; Brandizzi, Federica (April 2018, Methods in molecular biology)

   In plant cells, vacuoles are extremely important for growth and development, and influence important cellular functions as photosynthesis, respiration, and transpiration. Plant cells contain lytic and storage vacuoles, whose size can be different depending on cell type and tissue developmental stage. One of the main roles of vacuoles is to regulate the cell turgor in response to different stimuli. Thus, studying the morphology, dynamics, and physiology of vacuole is fundamentally important to advance knowledge in plant cell biology at large. The availability of fluorescent probes allows marking vacuoles in multiple ways. These may be fast, when using commercially available chemical dyes, or relatively slow, in the case of specific genetically encoded markers based on proteins directed either to the membrane of the vacuole (tonoplast) or to the vacuole lumen. Any of these approaches provides useful information about the morphology and physiology of the vacuole. 

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4. Phosphatidylinositol 3, 5‐bisphosphate regulates Ca ²⁺ transport during yeast vacuolar fusion through the Ca ²⁺ ATPase Pmc1

   https://doi.org/10.1111/tra.12736  

   Miner, Gregory E.; Sullivan, Katherine D.; Zhang, Chi; Rivera‐Kohr, David; Guo, Annie; Hurst, Logan R.; Ellis, Ez C.; Starr, Matthew L.; Jones, Brandon C.; Fratti, Rutilio A. (June 2020, Traffic)

   Abstract The transport of Ca²⁺across membranes precedes the fusion and fission of various lipid bilayers. Yeast vacuoles under hyperosmotic stress become fragmented through fission events that requires the release of Ca²⁺stores through the TRP channel Yvc1. This requires the phosphorylation of phosphatidylinositol‐3‐phosphate (PI3P) by the PI3P‐5‐kinase Fab1 to produce transient PI(3,5)P₂pools. Ca²⁺is also released during vacuole fusion upontrans‐SNARE complex assembly, however, its role remains unclear. The effect of PI(3,5)P₂on Ca²⁺flux during fusion was independent of Yvc1. Here, we show that while low levels of PI(3,5)P₂were required for Ca²⁺uptake into the vacuole, increased concentrations abolished Ca²⁺efflux. This was as shown by the addition of exogenous dioctanoyl PI(3,5)P₂or increased endogenous production of by the hyperactivefab1^T2250Amutant. In contrast, the lack of PI(3,5)P₂on vacuoles from the kinase deadfab1^EEEmutant showed delayed and decreased Ca²⁺uptake. The effects of PI(3,5)P₂were linked to the Ca²⁺pump Pmc1, as its deletion rendered vacuoles resistant to the effects of excess PI(3,5)P₂. Experiments with Verapamil inhibited Ca²⁺uptake when added at the start of the assay, while adding it after Ca²⁺had been taken up resulted in the rapid expulsion of Ca²⁺. Vacuoles lacking both Pmc1 and the H⁺/Ca²⁺exchanger Vcx1 lacked the ability to take up Ca²⁺and instead expelled it upon the addition of ATP. Together these data suggest that a balance of efflux and uptake compete during the fusion pathway and that the levels of PI(3,5)P₂can modulate which path predominates. 

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5. VPS45 is required for both diffuse and tip growth of Arabidopsis thaliana cells

   https://doi.org/10.3389/fpls.2023.1120307  

   Mugume, Yosia; Roy, Rahul; Agbemafle, William; Shepard, Gabriella N.; Vue, Yee; Bassham, Diane C. (February 2023, Frontiers in Plant Science)

   IntroductionVPS45 belongs to the Sec1/Munc18 family of proteins, which interact with and regulate Qa-SNARE function during membrane fusion. We have shown previously thatArabidopsis thalianaVPS45 interacts with the SYP61/SYP41/VTI12 SNARE complex, which locates on thetrans-Golgi network (TGN). It is required for SYP41 stability, and it functions in cargo trafficking to the vacuole and in cell expansion. It is also required for correct auxin distribution during gravitropism and lateral root growth. ResultsAsvps45knockout mutation is lethal in Arabidopsis, we identified a mutant,vps45-3, with a point mutation in theVPS45gene causing a serine 284-to-phenylalanine substitution. The VPS45-3 protein is stable and maintains interaction with SYP61 and SYP41. However,vps45-3plants display severe growth defects with significantly reduced organ and cell size, similar tovps45RNAi transgenic lines that have reduced VPS45 protein levels. Root hair and pollen tube elongation, both processes of tip growth, are highly compromised invps45-3. Mutant root hairs are shorter and thicker than those of wild-type plants, and are wavy. These root hairs have vacuolar defects, containing many small vacuoles, compared with WT root hairs with a single large vacuole occupying much of the cell volume. Pollen tubes were also significantly shorter invps45-3compared to WT. DiscussionWe thus show that VPS45 is essential for proper tip growth and propose that the observed vacuolar defects lead to loss of the turgor pressure needed for tip growth. 

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