Identification of a Rab GTPase-activating protein cascade that controls recycling of the Rab5 GTPase Vps21 from the vacuole

Transport within the endocytic pathway depends on a consecutive function of the endosomal Rab5 and the late endosomal/lysosomal Rab7 GTPases to promote membrane recycling and fusion in the context of endosomal maturation. We previously identified the hexameric BLOC-1 complex as an effector of the yeast Rab5 Vps21, which also recruits the GTPase-activating protein (GAP) Msb3. This raises the question of when Vps21 is inactivated on endosomes. We provide evidence for a Rab cascade in which activation of the Rab7 homologue Ypt7 triggers inactivation of Vps21. We find that the guanine nucleotide exchange factor (GEF) of Ypt7 (the Mon1-Ccz1 complex) and BLOC-1 both localize to the same endosomes. Overexpression of Mon1-Ccz1, which generates additional Ypt7-GTP, or overexpression of activated Ypt7 promotes relocalization of Vps21 from endosomes to the endoplasmic reticulum (ER), which is indicative of Vps21 inactivation. This ER relocalization is prevented by loss of either BLOC-1 or Msb3, but it also occurs in mutants lacking endosome–vacuole fusion machinery such as the HOPS tethering complex, an effector of Ypt7. Importantly, BLOC-1 interacts with the HOPS on vacuoles, suggesting a direct Ypt7-dependent cross-talk. These data indicate that efficient Vps21 recycling requires both Ypt7 and endosome–vacuole fusion, thus suggesting extended control of a GAP cascade beyond Rab interactions.     

The Msb3/Gyp3 GAP controls the activity of the Rab GTPases Vps21 and Ypt7 at endosomes and vacuoles

Fusion of organelles in the endomembrane system depends on Rab GTPases that interact with tethering factors before lipid bilayer mixing. In yeast, the Rab5 GTPase Vps21 controls fusion and membrane dynamics between early and late endosomes. Here we identify Msb3/Gyp3 as a specific Vps21 GTPase-activating protein (GAP). Loss of Msb3 results in an accumulation of Vps21 and one of its effectors Vps8, a subunit of the CORVET complex, at the vacuole membrane in vivo. In agreement, Msb3 forms a specific transition complex with Vps21, has the highest activity of all recombinant GAPs for Vps21 in vitro, and is found at vacuoles despite its predominant localization to bud tips and bud necks at the plasma membrane. Surprisingly, Msb3 also inhibits vacuole fusion, which can be rescued by the Ypt7 GDP-GTP exchange factor (GEF), the Mon1-Ccz1 complex. Consistently, msb3 vacuoles fuse more efficiently than wild-type vacuoles in vitro, suggesting that GAP can also act on Ypt7. Our data indicate that GAPs such as Msb3 can act on multiple substrates in vivo at both ends of a trafficking pathway. This ensures specificity of the subsequent GEF-mediated activation of the Rab that initiates the next transport event.     

Efficient termination of vacuolar Rab GTPase signaling requires coordinated action by a GAP and a protein kinase

Rab guanosine triphosphatases (GTPases) are pivotal regulators of membrane identity and dynamics, but the in vivo pathways that control Rab signaling are poorly defined. Here, we show that the GTPase-activating protein Gyp7 inactivates the yeast vacuole Rab Ypt7 in vivo. To efficiently terminate Ypt7 signaling, Gyp7 requires downstream assistance from an inhibitory casein kinase I, Yck3. Yck3 mediates phosphorylation of at least two Ypt7 signaling targets: a tether, the Vps-C/homotypic fusion and vacuole protein sorting (HOPS) subunit Vps41, and a SNARE, Vam3. Phosphorylation of both substrates is opposed by Ypt7-guanosine triphosphate (GTP). We further demonstrate that Ypt7 binds not one but two Vps-C/HOPS subunits: Vps39, a putative Ypt7 nucleotide exchange factor, and Vps41. Gyp7-stimulated GTP hydrolysis on Ypt7 therefore appears to trigger both passive termination of Ypt7 signaling and active kinase-mediated inhibition of Ypt7's downstream targets. We propose that signal propagation through the Ypt7 pathway is controlled by integrated feedback and feed-forward loops. In this model, Yck3 enforces a requirement for the activated Rab in docking and fusion.     

Membrane dynamics and fusion at late endosomes and vacuoles--Rab regulation, multisubunit tethering complexes and SNAREs

Membrane fusion at late endosomes and vacuoles depends on a conserved machinery, which includes Rab GTPases, their binding to tethering complexes and SNAREs. Fusion is initiated by the interaction of Rabs with tethering complexes. At the endosome, the CORVET complex interacts with the Rab5 GTPase Vps21, whereas the homologous HOPS complex binds the Rab7-like Ypt7 at the late endosome and vacuole. Activation of Ypt7 requires the recruitment of the Mon1-Ccz1 complex to the late endosome, which occurs via the CORVET complex. The interaction of Rab and the tethering complex is followed by the assembly of SNAREs, which leads to bilayer mixing. In this review, we will summarize our current knowledge on the mechanisms and regulation of endosome and vacuole membrane dynamics, and their role in organelle physiology.     

A Highlights from MBoC Selection: The casein kinases Yck1p and Yck2p act in the secretory pathway,in part,by regulating the Rab exchange factor Sec2p

Sec2p is a guanine nucleotide exchange factor that activates Sec4p, the final Rab GTPase of the yeast secretory pathway. Sec2p is recruited to secretory vesicles by the upstream Rab Ypt32p acting in concert with phosphatidylinositol-4-phosphate (PI(4)P). Sec2p also binds to the Sec4p effector Sec15p, yet Ypt32p and Sec15p compete against each other for binding to Sec2p. We report here that the redundant casein kinases Yck1p and Yck2p phosphorylate sites within the Ypt32p/Sec15p binding region and in doing so promote binding to Sec15p and inhibit binding to Ypt32p. We show that Yck2p binds to the autoinhibitory domain of Sec2p, adjacent to the PI(4)P binding site, and that addition of PI(4)P inhibits Sec2p phosphorylation by Yck2p. Loss of Yck1p and Yck2p function leads to accumulation of an intracellular pool of the secreted glucanase Bgl2p, as well as to accumulation of Golgi-related structures in the cytoplasm. We propose that Sec2p is phosphorylated after it has been recruited to secretory vesicles and the level of PI(4)P has been reduced. This promotes Sec2p function by stimulating its interaction with Sec15p. Finally, Sec2p is dephosphorylated very late in the exocytic reaction to facilitate recycling.     

Rab GTPase regulation of retromer-mediated cargo export during endosome maturation

The retromer complex, composed of sorting nexin subunits and a Vps26/Vps29/Vps35 trimer, mediates sorting of retrograde cargo from the endosome to the trans-Golgi network. The retromer trimer subcomplex is an effector of Rab7 (Ypt7 in yeast). Whereas endosome targeting of human retromer has been shown to require Rab7-GTP, targeting of yeast retromer to the endosome is independent of Ypt7-GTP and requires the Vps5 and Vps17 retromer sorting nexin subunits. An evolutionarily conserved amino acid segment within Vps35 is required for Ypt7/Rab7 recognition in vivo by both yeast and human retromer, establishing that Rab recognition is a conserved feature of this subunit. Recognition of Ypt7 by retromer is required for its function in retrograde sorting, and in yeast cells lacking the guanine nucleotide exchange factor for Ypt7, retrograde cargo accumulates in endosomes that are decorated with retromer, revealing an additional role for Rab recognition at the cargo export stage of the retromer functional cycle. In addition, yeast retromer trimer antagonizes Ypt7-regulated organelle tethering and fusion of endosomes/vacuoles via recognition of Ypt7. Thus retromer has dual roles in retrograde cargo export and in controlling the fusion dynamics of the late endovacuolar system.     

The HOPS/class C Vps complex tethers membranes by binding to one Rab GTPase in each apposed membrane

Many Rab GTPase effectors are membrane-tethering factors, that is, they physically link two apposed membranes before intracellular membrane fusion. In this study, we investigate the distinct binding factors needed on apposed membranes for Rab effector–dependent tethering. We show that the homotypic fusion and protein-sorting/class C vacuole protein-sorting (HOPS/class C Vps) complex can tether low-curvature membranes, that is, liposomes with a diameter of ∼100 nm, only when the yeast vacuolar Rab GTPase Ypt7p is present in both tethered membranes. When HOPS is phosphorylated by the vacuolar casein kinase I, Yck3p, tethering only takes place when GTP-bound Ypt7p is present in both tethered membranes. When HOPS is not phosphorylated, however, its tethering activity shows little specificity for the nucleotide-binding state of Ypt7p. These results suggest a model for HOPS-mediated tethering in which HOPS tethers membranes by binding to Ypt7p in each of the two tethered membranes. Moreover, because vacuole-associated HOPS is presumably phosphorylated by Yck3p, our results suggest that nucleotide exchange of Ypt7p on multivesicular bodies (MVBs)/late endosomes must take place before HOPS can mediate tethering at vacuoles.     

Phosphorylation of the effector complex HOPS by the vacuolar kinase Yck3p confers Rab nucleotide specificity for vacuole docking and fusion

The homotypic fusion of yeast vacuoles requires the Rab-family GTPase Ypt7p and its effector complex, homotypic fusion and vacuole protein sorting complex (HOPS). Although the vacuolar kinase Yck3p is required for the sensitivity of vacuole fusion to proteins that regulate the Rab GTPase cycle-Gdi1p (GDP-dissociation inhibitor [GDI]) or Gyp1p/Gyp7p (GTPase-activating protein)-this kinase phosphorylates HOPS rather than Ypt7p. We addressed this puzzle in reconstituted proteoliposome fusion reactions with all-purified components. In the presence of HOPS and Sec17p/Sec18p, there is comparable fusion of 4-SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteoliposomes when they have Ypt7p bearing either GDP or GTP, a striking exception to the rule that only GTP-bound forms of Ras-superfamily GTPases have active conformations. However, the phosphorylation of HOPS by recombinant Yck3p confers a strict requirement for GTP-bound Ypt7p for binding phosphorylated HOPS, for optimal membrane tethering, and for proteoliposome fusion. Added GTPase-activating protein promotes GTP hydrolysis by Ypt7p, and added GDI captures Ypt7p in its GDP-bound state during nucleotide cycling. In either case, the net conversion of Ypt7:GTP to Ypt7:GDP has no effect on HOPS binding or activity but blocks fusion mediated by phosphorylated HOPS. Thus guanine nucleotide specificity of the vacuolar fusion Rab Ypt7p is conferred through downstream posttranslational modification of its effector complex.     

Guanine Nucleotide Exchange Factors (GEFs) Have a Critical but Not Exclusive Role in Organelle Localization of Rab GTPases

Membrane fusion at eukaryotic organelles is initiated by Rab GTPases and tethering factors. Rabs in their GDP-bound form are kept soluble in the cytoplasm by the GDP dissociation inhibitor (GDI) chaperone. Guanine nucleotide exchange factors (GEFs) are found at organelles and are critical for Rab function. Here, we surveyed the overall role of GEFs in Rab localization. We show that GEFs, but none of the proposed GDI displacement factors, are essential for the correct membrane localization of yeast Rabs. In the absence of the GEF, Rabs lost their primary localization to the target organelle. Several Rabs, such as vacuolar Ypt7, were found at the endoplasmic reticulum and thus were still membrane-bound. Surprisingly, a Ypt7 mutant that undergoes facilitated nucleotide exchange localized to vacuoles independently of its GEF Mon1-Ccz1 and rescued vacuole morphology. In contrast, wild-type Ypt7 required its GEF for localization and to counteract the extraction by GDI. Our data agree with the emerging model that GEFs are critical for Rab localization but raise the possibility that additional factors can contribute to this process.     

The N-Terminal Domains of Vps3 and Vps8 Are Critical for Localization and Function of the CORVET Tethering Complex on Endosomes

Endosomal biogenesis depends on multiple fusion and fission events. For fusion, the heterohexameric CORVET complex as an effector of the endosomal Rab5/Vps21 GTPase has a central function in the initial tethering event. Here, we show that the CORVET-specific Vps3 and Vps8 subunits, which interact with Rab5/Vps21, require their N-terminal domains for localization and function. Surprisingly, CORVET may lack either one of the two N-terminal domains, but not both, to promote protein sorting via the endosome. The dually truncated complex mislocalizes to the cytosol and is impaired in endocytic protein sorting, but not in assembly. Furthermore, the endosomal localization can be rescued by overexpression of Vps21 or one of the truncated CORVET subunits, even though CORVET assembly is not impaired by loss of the N-terminal domains or in strains lacking all endosomal Rab5s and Ypt7. We thus conclude that CORVET requires only its C-terminal domains for assembly and has beyond its putative β-propeller domains additional binding sites for endosomes, which could be important to bind Vps21 and other endosome-specific factors for efficient endosome tethering.     

The Major Role of the Rab Ypt7p in Vacuole Fusion Is Supporting HOPS Membrane Association

Yeast vacuole fusion requires soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs), the Rab GTPase Ypt7p, vacuolar lipids, Sec17p and Sec18p, and the homotypic fusion and vacuole protein sorting complex (HOPS). HOPS is a multisubunit protein with direct affinities for SNAREs, vacuolar lipids, and the GTP-bound form of Ypt7p; each of these affinities contributes to HOPS association with the organelle. Using all-purified components, we have reconstituted fusion, but the Rab Ypt7p was not required. We now report that phosphorylation of HOPS by the vacuolar kinase Yck3p blocks HOPS binding to vacuolar lipids, making HOPS membrane association and the ensuing fusion depend on the presence of Ypt7p. In accord with this finding in the reconstituted fusion reaction, the inactivation of Ypt7p by the GTPase-activating protein Gyp1–46p only blocks the fusion of purified vacuoles when Yck3p is present and active. Thus, although Ypt7p may contribute to other fusion functions, its central role is to bind HOPS to the membrane.Rab proteins are small GTP-binding proteins involved in multiple steps of membrane traffic, including protein sorting, vesicle transport, and SNARE³-dependent membrane fusion (1). Rabs in their GTP-bound state bind proteins that are essential for mediating Rab function, which are therefore termed “effectors.” These effectors are diverse and perform various biochemical functions. For membrane fusion, Rabs and their effectors support tethering, the initial membrane contact that is needed for the subsequent assembly of trans-SNARE complexes between membranes (1, 2). A central question in organelle trafficking, which we now address, is whether Rabs are only required for binding their effectors to the membrane or whether they also activate the bound effector or provide some additional essential function for membrane fusion.We study membrane fusion using isolated yeast vacuoles (3). Yeast vacuole fusion requires the Rab GTPase Ypt7p, the heterohexameric HOPS complex, four vacuolar SNAREs, the SNARE disassembly chaperones Sec17p and Sec18p, and chemically minor yet functionally essential lipids, termed “regulatory” lipids. The HOPS complex is an effector of Ypt7p (4) and belongs to a group of functionally conserved large multisubunit tethering complexes, many of which are Rab effectors (5). The Vps39p subunit of HOPS is a nucleotide exchange factor for Ypt7p (6). HOPS is also a SNARE chaperone; its Vps33p subunit is a Sec1p/Munc18-1 family (SM) protein, HOPS binds multiple vacuolar SNAREs (7–9), and it proofreads SNARE complex structure (10). HOPS also binds to specific phosphoinositides (8), and these are among the regulatory lipids that are important for fusion (11–13).We have recently reconstituted membrane fusion using proteoliposomes of pure vacuolar proteins and lipids (13). HOPS and the regulatory lipids are crucial for rapid fusion of proteoliposome pairs bearing the three Q-SNAREs on one proteoliposome and the R-SNARE on the other and are absolutely required when all four SNAREs are present on each proteoliposome and Sec17p and Sec18p are present. Ypt7p is not required, showing that HOPS can stimulate SNARE-dependent fusion in vitro even in the absence of its Rab, although Ypt7p stimulates the fusion of these proteoliposomes.4Yeast vacuole fusion can be negatively regulated either by GTPase-activating proteins (GAPs) (14, 15) that promote GTP hydrolysis by Ypt7p or by the kinase Yck3p, which phosphorylates the Vps41p subunit of HOPS (16) and the vacuolar SNARE Vam3p (15). Yck3p is a palmitoylated (17), vacuole-localized kinase of the casein kinase I family (18). The complete fragmentation of vacuoles in vivo, indicating a block of fusion, requires both Ypt7p inactivation by a RabGAP and the presence of Yck3p (15). Yck3p is necessary for efficient vacuole inheritance (16) and normal vacuole morphology (19), suggesting that its function is part of the normal mechanism of vacuole segregation during the cell cycle. Although Yck3p clearly regulates vacuole fusion through phosphorylation of HOPS, it remains unclear which activities of HOPS are inhibited by Yck3p phosphorylation and whether Yck3p must also phosphorylate other vacuole fusion proteins such as Vam3p to block fusion.We now show that phosphorylation of the Vps41p subunit of HOPS by purified Yck3p reduces HOPS binding to membrane lipids, thereby making HOPS association with the membrane and the ensuing fusion of reconstituted proteoliposomes dependent on active Ypt7p. These data with proteoliposomes are supported by assays with purified vacuoles; the RabGAP Gyp1–46p only inhibits the in vitro fusion of yck3Δ vacuoles when purified Yck3p is added. As for Ypt7p and HOPS, the major function of other Rabs may also be to act as membrane receptors for their effectors.     

The vacuolar kinase Yck3 maintains organelle fragmentation by regulating the HOPS tethering complex

The regulation of cellular membrane flux is poorly understood. Yeast respond to hypertonic stress by fragmentation of the normally large, low copy vacuole. We used this phenomenon as the basis for an in vivo screen to identify regulators of vacuole membrane dynamics. We report here that maintenance of the fragmented phenotype requires the vacuolar casein kinase I Yck3: when Yck3 is absent, salt-stressed vacuoles undergo fission, but reassemble in a SNARE-dependent manner, suggesting that vacuole fusion is disregulated. Accordingly, when Yck3 is deleted, in vitro vacuole fusion is increased, and Yck3 overexpression blocks fusion. Morphological and functional studies show that Yck3 modulates the Rab/homotypic fusion and vacuole protein sorting complex (HOPS)-dependent tethering stage of vacuole fusion. Intriguingly, Yck3 mediates phosphorylation of the HOPS subunit Vps41, a bi-functional protein involved in both budding and fusion during vacuole biogenesis. Because Yck3 also promotes efficient vacuole inheritance, we propose that tethering complex phosphorylation is a part of a general, switch-like mechanism for driving changes in organelle architecture.     

Yeast vacuolar HOPS,regulated by its kinase,exploits affinities for acidic lipids and Rab:GTP for membrane binding and to catalyze tethering and fusion

Fusion of yeast vacuoles requires the Rab GTPase Ypt7p, four SNAREs (soluble N-ethylmaleimide–sensitive factor attachment protein receptors), the SNARE disassembly chaperones Sec17p/Sec18p, vacuolar lipids, and the Rab-effector complex HOPS (homotypic fusion and vacuole protein sorting). Two HOPS subunits have direct affinity for Ypt7p. Although vacuolar fusion has been reconstituted with purified components, the functional relationships between individual lipids and Ypt7p:GTP have remained unclear. We now report that acidic lipids function with Ypt7p as coreceptors for HOPS, supporting membrane tethering and fusion. After phosphorylation by the vacuolar kinase Yck3p, phospho-HOPS needs both Ypt7p:GTP and acidic lipids to support fusion.     

The vacuolar V1/V0-ATPase is involved in the release of the HOPS subunit Vps41 from vacuoles, vacuole fragmentation and fusion

At yeast vacuoles, phosphorylation of the HOPS subunit Vps41 depends on the Yck3 kinase. In a screen for mutants that mimic the yck3Delta phenotype, in which Vps41 accumulates in vacuolar dots, we observed that mutants in the V0-part of the V0/V1-ATPase, in particular in vma16Delta, also accumulate Vps41. This accumulation is not due to a phosphorylation defect, but to reduced release of Vps41 from vma16Delta vacuoles. One reason could be a connection to vacuole fission, which is blocked in V-ATPase mutants. Vacuole fusion is not impaired between vacuoles lacking the V0-subunits Vma16 or Vma6 and wild-type vacuoles, whereas fusion between mutant vacuoles is reduced. Our data suggest a connection between vacuole biogenesis and membrane fusion.     

Vps9 Family Protein Muk1 Is the Second Rab5 Guanosine Nucleotide Exchange Factor in Budding Yeast

VPS9 domains can act as guanosine nucleotide exchange factors (GEFs) against small G proteins of the Rab5 family. Saccharomyces cerevisiae vps9Δ mutants have trafficking defects considerably less severe than multiple deletions of the three cognate Rab5 paralogs (Vps21, Ypt52, and Ypt53). Here, we show that Muk1, which also contains a VPS9 domain, acts as a second GEF against Vps21, Ypt52, and Ypt53. Muk1 is partially redundant with Vps9 in vivo, with vps9Δ muk1Δ double mutant cells displaying hypersensitivity to temperature and ionic stress, as well as profound impairments in endocytic and Golgi endosome trafficking, including defects in sorting through the multivesicular body. Cells lacking both Vps9 and Muk1 closely phenocopy double and triple knock-out strains lacking Rab5 paralogs. Microscopy and overexpression experiments demonstrate that Vps9 and Muk1 have distinct localization determinants. These experiments establish Muk1 as the second Rab5 GEF in budding yeast.     

Who’s in control? Principles of Rab GTPase activation in endolysosomal membrane trafficking and beyond

The eukaryotic endomembrane system consists of multiple interconnected organelles. Rab GTPases are organelle-specific markers that give identity to these membranes by recruiting transport and trafficking proteins. During transport processes or along organelle maturation, one Rab is replaced by another, a process termed Rab cascade, which requires at its center a Rab-specific guanine nucleotide exchange factor (GEF). The endolysosomal system serves here as a prime example for a Rab cascade. Along with endosomal maturation, the endosomal Rab5 recruits and activates the Rab7-specific GEF Mon1-Ccz1, resulting in Rab7 activation on endosomes and subsequent fusion of endosomes with lysosomes. In this review, we focus on the current idea of Mon1-Ccz1 recruitment and activation in the endolysosomal and autophagic pathway. We compare identified principles to other GTPase cascades on endomembranes, highlight the importance of regulation, and evaluate in this context the strength and relevance of recent developments in in vitro analyses to understand the underlying foundation of organelle biogenesis and maturation.

Membrane identity in the endomembrane systemOne key feature of eukaryotic cells is the presence of membrane-enclosed organelles, which constantly exchange proteins, lipids, or metabolites via vesicular transport or membrane contact sites (MCSs). Along the endomembrane system, vesicular trafficking requires vesicle budding from the donor membrane and directed transport toward and fusion with the acceptor compartment. The resulting trafficking routes form a regulated network that connects not only the internal organelles, but also the interior and exterior of the cell.The specific identity of organelles within the endomembrane system is defined by the lipid and protein composition of their membranes. This includes signaling lipids such as phosphoinositides (PIPs) and small GTPases of the Ras superfamily of small G proteins, namely of the Rab, Arf, and Arl families, which act as binding platforms for accessory proteins involved in multiple membrane trafficking processes (Balla, 2013).Rab GTPases, like other small GTPases, are key regulatory proteins that switch between an inactive GDP-bound (Rab-GDP) and an active GTP-bound (Rab-GTP) state (Barr, 2013; Goody et al., 2017; Hutagalung and Novick, 2011). Rabs are posttranslationally modified by the addition of geranylgeranyl moieties to C-terminal cysteine residues, which allow their reversible membrane association. Within the cytosol, Rab-GDP is kept soluble by binding to the chaperone-like GDP dissociation inhibitor (GDI). At the target membrane, an organelle-specific guanine nucleotide exchange factor (GEF) activates the Rab after its previous release from GDI, a process possibly supported by other factors (Dirac-Svejstrup et al., 1997). GTP binding stabilizes two loops in the Rab GTPase domain, which allows recruitment and binding of various so-called effector proteins to the Rab-GTP on the membrane. Rab GTPases are inefficient enzymes with a low intrinsic GTP hydrolysis rate and thus depend on a GTPase-activating protein (GAP) to hydrolyze bound GTP. GDI then extracts the Rab-GDP and keeps it soluble in the cytosol until the next activation cycle (Barr, 2013; Goody et al., 2017; Hutagalung and Novick, 2011). In addition to their conserved GTPase domain, Rabs contain a hypervariable C-terminal domain (HVD), which supports GEF recognition and therefore correct localization of the Rab (Thomas et al., 2018)Among various other functions, Rab GTPases are critical for the fusion of vesicles with the acceptor membrane by recruiting tethering proteins, which bring the two membranes into close proximity. Tethers, together with Sec1/Munc18 proteins, promote the folding of membrane-bound SNAREs at the vesicle and the target membrane into tetrameric coiled-coil complexes. This process further reduces the distance between the membranes, bypasses the hydration layer on membranes, and results in mixing of lipid bilayers and consequently membrane fusion (Wickner and Rizo, 2017; Ungermann and Kümmel, 2019).Organization and function of the endolysosomal pathwayEndocytosis allows the rapid adaptation of plasma membrane composition in response to changing environmental conditions by the uptake of membrane proteins from the plasma membrane, which are either transported to and finally degraded in the lysosome or sorted back to the plasma membrane, e.g., receptors after releasing their cargo within the endosomal lumen (Sardana and Emr, 2021). A third fate of endocytosed cargo is trafficking to the Golgi (Laidlaw and MacDonald, 2018). In addition, various kinds of endocytosis allow the uptake of very large particles such as bacteria during phagocytosis or fluids during pinocytosis (Huotari and Helenius, 2011; Babst, 2014). The endocytic pathway is also involved in the quality control system of plasma membrane proteins and allows degradation of damaged cell surface proteins as well as the down-regulation of nutrient transporters and receptors (Sardana and Emr, 2021). During endocytosis, membrane proteins marked by ubiquitination are incorporated into endocytic vesicles, which pinch off the plasma membrane and fuse with the tubular-shaped early endosome (EE) in the cell periphery (Fig. 1 A). The EE serves as a sorting station, at which membrane proteins are either sorted into tubular structures and brought to the recycling endosome (RE) or get incorporated into intraluminal vesicles (ILVs) with the help of four endosomal sorting complexes required for transport (ESCRTs; Sardana and Emr, 2021). A prerequisite for the degradation of cargo in the lysosome is the maturation of EEs into late endosomes (LEs) by changing the organelle surface composition, including specific Rab GTPases and PIPs, and organelle shape. The LE is eventually spherically shaped, containing multiple ILVs and a more acidified lumen. Therefore, it is also called Multivesicular Body (MVB). Upon fusion with the lysosome, ILVs and their content are degraded into precursor molecules, which are reused by the cell (Fig. 1 A; Sardana and Emr, 2021; Huotari and Helenius, 2011).Open in a separate windowFigure 1.Rab GTPases in the endolysosomal pathway.(A) Localization of key Rab GTPases along the endolysosomal pathway. Endocytic vesicles containing cargo (blue dot) or receptor proteins (red) are substrates of endocytosis. Endocytic vesicles (EV) fuse with the EE. Rabs are shown by numbers: Rab5 (green) on early EE is replaced by Rab7 (black) on multivesicular bodies (MVBs). GEFs are shown in blue. Positioning of lysosomes (Lys) depends on binding to motor proteins by either Arl8b (orange, 8b) or Rab7. Recycling occurs via REs involving Rab4, Rab11, and Rab14. MTOC, microtubule organizing center; Nuc, nucleus. (B) Spatiotemporal Rab5-to-Rab7 transition during endosomal maturation. Rab5 (green graph) is rapidly recruited to EE and replaced by Rab7. (C) Model of Rab7 GEF recruitment and activation on endosomes. Mon1-Ccz1 (or the trimeric complex additionally containing Rmc1/C18orf8/Bulli, as indicated by the unlabeled hexagon) requires Rab5-GTP for activation to promote Rab7 recruitment. For details, see text.Central functions of Rab5 and Rab7Along the endolysosomal system, several Rabs coordinate sorting and recycling processes at the EE and LE. Early endosomal Rab5 and late endosomal Rab7 are here the key Rabs conserved among species. Their spatiotemporal activation and therefore functions are tightly coordinated on the level of the MVB/LE (Fig. 1 B).In yeast, the Rab5-like GTPases Vps21, Ypt52, Ypt52, and Ypt10 and the Rab7-like Ypt7 structure the endocytic pathway (Singer-Krüger et al., 1994; Wichmann et al., 1992). In mammalian cells, Rab5 (with Rab5a, b, and c isoforms having nonredundant functions in the endocytic network; Chen et al., 2014, 2009) and Rab7 (with Rab7a and b isoforms, of which Rab7a is the main actor in transport processes along the endocytic pathway [Guerra and Bucci, 2016], whereas Rab7b has a role in the transport from endosome to the Golgi [Kjos et al., 2017; Progida et al., 2010]) are present (Wandinger-Ness and Zerial, 2014). While the overall organization of the endocytic pathway into EE and LE is conserved, yeast seems to have a more ancestral minimal endomembrane system, where the trans-Golgi network acts as EE and RE (Day et al., 2018). In mammalian cells, the more complex endolysosomal system depends on additional Rabs. Rab4 is involved in protein sorting at the EE, activation of Rab5, and recycling of cargo back to the plasma membrane (Kälin et al., 2015; Wandinger-Ness and Zerial, 2014; de Renzis et al., 2002), whereas Rab11 and Rab14 function at REs (Fig. 1 A; Linford et al., 2012; Takahashi et al., 2012). Furthermore, Rab9 is required for retrograde transport between LEs and the trans-Golgi network (Lombardi et al., 1993), and Rab32 and Rab38 function in the biogenesis of lysosome-related organelles (Bowman et al., 2019; Gerondopoulos et al., 2012; Wasmeier et al., 2006).During endosomal maturation, Rab5 is exchanged for Rab7 (Rink et al., 2005; Poteryaev et al., 2010). This Rab switch is highly conserved and a prime example of coordinated Rab turnover during organelle maturation. The rapid transition from Rab5 to Rab7 was explained by a so-called cutout switch, where activation of Rab5 fosters at a threshold value activation of Rab7, which in turn suppresses further Rab5 activation (Fig. 1 B; Del Conte-Zerial et al., 2008). Such a principle may apply to most Rab cascades (Barr, 2013).Rab5 has multiple functions on EEs (Wandinger-Ness and Zerial, 2014). It interacts with a number of effectors such as the lipid kinase Vps34, Rabaptin-5, which is found in complex with the Rab5-GEF Rabex5, Rabenosyn-5, and tethers such as the class C core vacuole/endosome tethering (CORVET) complex or EEA1. Therefore, Rab5 is critical for the homotypic fusion of EEs (Gorvel et al., 1991; Ohya et al., 2009; Christoforidis et al., 1999a, b; Perini et al., 2014; Marat and Haucke, 2016). Vps34 was initially identified in yeast (Schu et al., 1993) and exists in two heterotetrametric complexes, which differ by just one subunit (Kihara et al., 2001). Complex I resides on autophagosomes, whereas complex II functions on endosomes (Fig. 2 D). Both complexes generate a local pool of phosphatidylinositol-3-phosphate (PI3P), to which several effectors bind, including the early endosomal tether EEA1 and ESCRTs (Wallroth and Haucke, 2018). Recent structural insights revealed that Rab5 recruits and activates endosomal complex II, whereas Rab1 acts similarly on autophagosomal complex I (Tremel et al., 2021). This explains how Rab5-GTP promotes the formation of a local endosomal PI3P pool (Franke et al., 2019). Interestingly, Caenorhabditis elegans VPS-34 can recruit the Rab5 GAP TBC-2 to endosomal membranes, suggesting a possible link between PI3P generation and Rab5 inactivation (Law et al., 2017).Open in a separate windowFigure 2.Rab7 activation on autophagosomes.(A and B) Atg8-dependent Mon1-Ccz1 recruitment and activation. Atg8 (violet) recruits Mon1-Ccz1 (and likely also the trimeric GEF complex in higher eukaryotes, as indicated by the unlabeled hexagon) and allows fusion with lysosome. (C) Model of spatiotemporal Rab7 activation on autophagosomes. Maturation is prerequisite for successful fusion. (D) Comparison of proteins involved in maturation of LEs and autophagosomes.Rab7 is a key component in the late endocytic pathway (Langemeyer et al., 2018a). It is found on LEs, lysosomes, and autophagosomes and is required for the biogenesis and positioning of LEs and lysosomes, for MCSs of lysosomes with other organelles, and for the fusion of endosomes and autophagosomes with lysosomes (Fig. 1 A; Guerra and Bucci, 2016; McEwan et al., 2015; Ballabio and Bonifacino, 2020; Cabukusta and Neefjes, 2018). Even though both the metazoan Rab7 and yeast Ypt7 are activated by the homologous Mon1-Ccz1 GEF complex and are required for endosomal maturation, their function on LEs and lysosomes is not entirely conserved. In yeast, active Ypt7 directly binds the hexameric homotypic fusion and vacuole protein sorting (HOPS) tethering complex and mediates SNARE-dependent fusion of LEs or autophagosomes with vacuoles as well as homotypic vacuole fusion (Wickner and Rizo, 2017; Gao et al., 2018a, b). In higher eukaryotes, HOPS also promotes fusion between LEs and lysosomes, yet apparently does not directly interact with Rab7, but rather with the GTPases Rab2 and Arl8b (Gillingham et al., 2014; Fujita et al., 2017; Lőrincz et al., 2017; Khatter et al., 2015). How Rab7 contributes to fusion at the lysosome is still unclear. Rab7 interacts with several proteins on lysosomes, including the cholesterol sensor ORPL1 and the dynein-interacting lysosomal RILP (Jordens et al., 2001; Cantalupo et al., 2001; Rocha et al., 2009). Both proteins also bind HOPS (van der Kant et al., 2015, 2013), as does another multivalent adaptor protein, PLEKHM1 (McEwan et al., 2015), which binds both Arl8b and Rab7 (Marwaha et al., 2017). Interestingly, Arl8b in complex with its effector SKIP also binds TBC1D15, a Rab7 GAP, which may displace Rab7 from LEs before their fusion with lysosomes (Jongsma et al., 2020). It is thus possible that fusion of LEs and autophagosomes with lysosomes requires a complex coordination of the three GTPases, Rab7, Arl8b, and Rab2, with the HOPS complex and other effectors. Some of this complexity may be explained by a second function of Rab7 and Arl8b in binding adapters of the kinesin or dynein motor protein family, which connect LEs and lysosomes to the microtubule network. Thereby Rab7 and Arl8b control the positioning of these organelles to the periphery or perinuclear area via the microtubule network, which has functional implications (Fig. 1 A; Cabukusta and Neefjes, 2018; Bonifacino and Neefjes, 2017). Perinuclear lysosomes are the main places for degradation of cargo delivered by endosomes and autophagosomes, whereas peripheral lysosomes are involved in the regulation of mammalian target of rapamycin complex1 (mTORC1), the master regulator switching between cell growth and autophagy (Johnson et al., 2016; Korolchuk et al., 2011). This also may be connected to the role of lysosomes in lipid homeostasis, as Rab7 seems to control cholesterol export via the lysosomal NPC1 (van den Boomen et al., 2020; Shin and Zoncu, 2020; Castellano et al., 2017). How far the acidification state of perinuclear and peripheral lysosomes also affects their Rab7 and Arl8b mediated localization is still under debate (Ponsford et al., 2021). Thus, it is likely that Rab7 coordinates LE and lysosomal transport and fusion activity in coordination with endosomal biogenesis and cellular metabolism.GEF function and regulation in endosomal maturationThe heterodimeric complex Mon1-Ccz1 was identified as the GEF for Ypt7 in yeast and for Rab7 in higher eukaryotes (Nordmann et al., 2010; Gerondopoulos et al., 2012). The Mon1-Ccz1 complex is an effector of Rab5 (Kinchen and Ravichandran, 2010; Langemeyer et al., 2020; Cui et al., 2014; Li et al., 2015; Poteryaev et al., 2010; Singh et al., 2014), suggesting a direct link to endosomal maturation and Rab turnover (Fig. 1 B). Structural analyses uncovered how the two central longin domains in Mon1 and Ccz1 displace the bound nucleotide from Ypt7 (Kiontke et al., 2017). Unlike yeast, the metazoan Mon1-Ccz1 complex contains a third subunit termed RMC1 or C18orf8 in mammals and Bulli in Drosophila (Vaites et al., 2017; Dehnen et al., 2020; van den Boomen et al., 2020). Even though loss of this subunit impairs endosomal and autophagosomal biogenesis, this subunit does not affect GEF activity toward Rab7 in vitro (Dehnen et al., 2020; Langemeyer et al., 2020), indicating that the general GEF mechanism is conserved across species. As Rab7 is required on LEs, autophagosomes, and lysosomes, spatial recruitment and activity of the Rab7 GEF must be tightly regulated.Rab5 activates the Mon1-Ccz1 GEF complexDuring endosomal maturation, the Mon1-Ccz1 complex is recruited to Rab5- and PI3P-positive endosomes and activates Rab7 for subsequent fusion of endosomes with lysosomes (Nordmann et al., 2010; Poteryaev et al., 2010; Cabrera and Ungermann, 2013; Cabrera et al., 2014; Singh et al., 2014; Fig. 1 C). However, it was postulated that (but remained unclear how) Rab5 affects Rab7 GEF activity. The activity of GEFs is in the simplest way determined in solution, where the respective Rab, which has been loaded with a fluorescent- or radioactive-labeled nucleotide, is incubated with the GEF (Schoebel et al., 2009; Bergbrede et al., 2009). GDP or GTP addition then triggers displacement of the bound nucleotide, which results in a decrease of fluorescence or increase of radioactive signal in solution. Such in-solution assays can uncover the Rab specificity of GEFs yet cannot recapitulate the membrane context and potential regulating factors. Recent approaches therefore used liposomes and prenylated Rab:GDI complexes to address the role of membrane lipids and proteins in GEF activation (Thomas and Fromme, 2016; Thomas et al., 2018; Langemeyer et al., 2020, 2018b; Cezanne et al., 2020; Bezeljak et al., 2020). Details of these reconstituted systems are discussed below. In yeast, prenylated, membrane-bound, and GTP-loaded Rab5-like Vps21 was surprisingly inefficient as a single factor to recruit Mon1-Ccz1 to membranes, whereas addition of PIPs together with Vps21 enhanced recruitment (Langemeyer et al., 2020). However, activity of both the yeast and metazoan Rab7 GEF complexes showed a striking dependence on membrane-bound Rab5-GTP in the GEF assay, whereas PIPs alone were not sufficient to drive GEF activation. These observations demonstrate that the Mon1-Ccz1 complex depends on membrane-bound Rab5 for its Rab7 GEF activity, which nicely explains some of the previous in vivo observations on endosomal Rab5-to-Rab7 exchange (Poteryaev et al., 2010; Rink et al., 2005).This Rab exchange, which occurs similarly on phagosomes (Jeschke and Haas, 2016), is in vivo likely regulated in space and time. Time-lapse microscopy studies revealed that levels of fluorescently labeled Rab5 decreased, while fluorescently labeled Rab7 increased on the surface of a tracked endosome (Poteryaev et al., 2010; Yasuda et al., 2016). Analysis of the spatiotemporal Rab5-to-Rab7 transition in mammalian cells revealed that Rab5-positive endosomes can separate from Rab7-positive membranes, suggesting that a stepwise maturation process also occurs in some cells (Skjeldal et al., 2021). However, in all cases, only some insights on Mon1-Ccz1 regulation are presently available. Phosphorylation is one potential regulatory mechanism in GEF regulation (Kulasekaran et al., 2015). Indeed, yeast Mon1-Ccz1 is a substrate of the vacuolar casein kinase 1 Yck3 (Lawrence et al., 2014). When added to the Rab5-dependent GEF assay, Yck3-mediated phosphorylation inhibited Mon1-Ccz1 GEF activity, presumably by blocking the Rab5 interaction (Langemeyer et al., 2020). How the kinase is in turn regulated and whether this is the only mechanism of Mon1-Ccz1 GEF control is currently unknown.Rab7 activation and function in autophagyThe lysosome is also the destination of the autophagic catabolic pathway. During autophagy, portions of the cytosol, specific organelles, aggregates, or pathogens are engulfed into a double-layered membrane, which upon closure fuses with the lysosome for degradation and reuse of its content (Fig. 2 A; Zhao and Zhang, 2019; Nakatogawa, 2020). Autophagy is a versatile pathway required for adaptation of a cell’s organelle repertoire and quality control.Rab7 is found not just on LEs, but also on autophagosomes (Hegedűs et al., 2016; Gao et al., 2018a), although its precise function seems to differ between organisms (Kuchitsu and Fukuda, 2018). In yeast, the Rab7-homologue Ypt7 mediates HOPS-dependent fusion of autophagosomes with vacuoles (Gao et al., 2018a). In metazoan cells, Rab7 and its effectors PLEKHM1 and WDR91 are required for autolysosome/amphisome-lysosome fusion, yet Rab7 does not seem to directly bind HOPS during fusion of autophagosomes with lysosomes (Xing et al., 2021; McEwan et al., 2015; Gutierrez et al., 2004; Kuchitsu and Fukuda, 2018).Given the striking Rab5 dependence on endosomes in Mon1-Ccz1 activation, the question arises, how does Mon1-Ccz1-mediated Rab7 activation happen on autophagosomes? Some data suggest that yeast and metazoan Rab5 is directly involved in the autophagy process such as autophagosome closure (Ravikumar et al., 2008; Bridges et al., 2012; Zhou et al., 2019, 2017), whereas others do not find direct evidence, for instance in Drosophila (Hegedűs et al., 2016). Studies in yeast revealed that the LC3–like Atg8 protein directly binds and recruits Mon1-Ccz1 to the autophagosomal membrane during starvation, which results in Ypt7 activation as a prerequisite of HOPS-dependent fusion with the vacuole (Gao et al., 2018a; Fig. 2 B). Tight regulation of Mon1-Ccz1 GEF-activity is apparently mandatory to avoid fusion of premature autophagosomes with the vacuole (Fig. 2 C). How Mon1-Ccz1 localization to either endosomes or autophagosomes is coordinated (also with regard to similarities in organelle features; Fig. 2 D) and whether Atg8/LC3 also regulates the activity of the GEF complex are not yet known.Of note, an endosomal-like Rab5-to-Rab7 cascade also occurs on the mitochondrial outer membrane during mitophagy in metazoan cells, a selective pathway to degrade damaged mitochondria (Yamano et al., 2018). Here, Rab5 is activated by a mitochondrially localized Rab5 GEF, followed by Mon1-Ccz1 recruitment and Rab7A activation, which then orchestrates the subsequent mitophagy process. How this process is coupled to autophagosome maturation, and whether Rab7 is then again needed on the formed autophagosome, has not been addressed so far.These data nevertheless demonstrate the adjustable recruitment of Mon1-Ccz1 during endosomal maturation and autophagosome formation and even to the mitochondrial surface. Targeting of the Mon1-Ccz1 complex is likely coordinated between all these processes.A role for ER-endosome MCSs in endosome maturationEndosomes form MCSs with the ER. Such contact sites have multiple roles ranging from lipid transport to ion exchange (Scorrano et al., 2019; Reinisch and Prinz, 2021). The endosome-ER contact depends on Rab7 and contributes to transport and positioning of endosomes, supports endosomal fission, and facilitates endocytic cargo transport and cholesterol transfer between LEs and the ER (Rocha et al., 2009; Friedman et al., 2013; Rowland et al., 2014; Raiborg et al., 2015; Jongsma et al., 2016). Rab7 activation via the Mon1-Ccz1 complex is required for cholesterol export from the lysosome, likely in the context of MCSs. Rab7 binds to the NPC1 cholesterol transporter and may thus promote cholesterol export only at MCSs with the ER or other organelles (van den Boomen et al., 2020). The ER is also involved in endosome maturation, which requires an MCS between Reticulon-3L on the ER and endosomal Rab9. In fact, Rab9 is recruited shortly before the Rab5-to-Rab7 transition (Wu and Voeltz, 2021; Kucera et al., 2016). How Rab9 activation and MCS formation are coordinated with endosomal maturation has not yet been revealed. It is likely that the spatial positioning of endosomes (Fig. 1 A), their acidification, and TORC1 activity also contribute to this process (Bonifacino and Neefjes, 2017; Johnson et al., 2016).Retromer opposes Rab7 activationRetromer is a conserved heteropentameric complex that mediates the formation of vesicular carriers at the endosome and thus allows the transport of receptors back to the Golgi or plasma membrane. The complex consists of a trimeric core (Vps35, Vps26, and Vps29), which binds either a SNX1-SNX4 heterodimer or a SNX3 monomer (Simonetti and Cullen, 2018; Leneva et al., 2021; Kovtun et al., 2018). Retromer is an effector of Rab7, but also recruits the Rab7 GAP TBC1D5 in metazoan cells (Rojas et al., 2008; Kvainickas et al., 2019; Jimenez-Orgaz et al., 2018; Distefano et al., 2018; Seaman et al., 2009). This dual function of retromer may facilitate the formation of endosomal tubules after the Rab5-to-Rab7 transition, and these tubules eventually lose Rab7 once scission has occurred (Jongsma et al., 2020).It is not yet clear how conserved the Rab7-retromer-GAP connection is. Yeast retromer is also an effector of the Rab7-like Ypt7 and coordinates protein recycling at the endosome (Liu et al., 2012; Balderhaar et al., 2010), yet a role of a Rab7 GAP has not been described. However, yeast retromer also binds to the Rab5 GEFs Vps9 and Muk1 (Bean et al., 2015), which suggests that both Rab5 and Rab7 function contribute to efficient tubule formation at the endosome. Whether and how the Rab7 GEF Mon1-Ccz1 is functionally coordinated with retromer will be a topic of future studies.GEF regulation along the endomembrane systemIn the previous section, we focused mainly on the role of the Rab7 GEF in the context of endosome and autophagosome maturation. However, the timing of GEF activation and the subsequent recruitment of their target Rabs is critical for all membrane trafficking processes along the endomembrane system to guarantee maintenance of intracellular organelle organization. Rabs in turn interact with effectors, and effectors such as the lysosomal HOPS complex not only bind SNAREs but also catalyze their assembly and thus drive membrane fusion (Fig. 3 A). The spatiotemporal regulation of GEF activation is therefore at the heart of organelle biogenesis and maturation, and thus membrane trafficking. Within this section, we will now broaden our view by comparing different regulatory principles of GEFs.Open in a separate windowFigure 3.Regulatory mechanisms influence the activity of GEFs.(A) Hierarchical cascade of factors controlling membrane fusion. GEFs integrate various signals and initiate a cascade of protein activities, finally leading to membrane fusion. Signaling lipids, the presence of cargo proteins, upstream GTPases, and kinases influence the activity of GEFs and therefore determine Rab GTPase activation. Consequently, effector proteins such as tethering factors are recruited. This ultimately leads to SNARE-mediated lipid bilayer mixing and membrane fusion. (B) A Rab cascade in yeast exocytosis. Active Ypt32 and PI4P (yellow) on late Golgi compartments and secretory vesicles recruit the GEF Sec2, which in turn promotes activation and stable membrane insertion of the Rab Sec4. (C) Mon1-Ccz1 regulation by phosphorylation. Mon1-Ccz1 is recruited to and activated on LEs by coincidence detection of membrane-associated Rab5 and PI3P (red, Fig. 1 C) and promotes stable membrane insertion of Rab7. This process is terminated by Mon1-Ccz1 phosphorylation by the type I casein kinase Yck3 in yeast (orange). (D) A positive feedback loop of GEF activation on endocytic vesicles and EEs. The Rab5 GEF Rabex-5 binds ubiquitinated cargo on endocytic vesicles and is autoinhibited. Rab5 recruits Rabaptin-5, which binds Rabex-5 and releases the GEF from autoinhibition, generating a positive feedback loop. (E) Membrane factors determine GEF activity of TRAPPII at the trans-Golgi. TRAPPII activity for the Rab Ypt32 requires membrane-associated Arf1 and PI4P. (F) The length of the hypervariable domain of Golgi Rabs defines the substrate specificity for TRAPP complexes. The yeast Rab GTPases Ypt1 and Ypt32 differ in the length of their C-terminal HVD (box). TRAPPII and TRAPPIII complexes have the same active site, which is positioned away from the membrane, and thus discriminate Rab accessibility. (G) Phosphorylation as a mechanism to promote GEF activity. DENND1 GEF activity is autoinhibited, which is released by Akt-mediated phosphorylation. For details, see text.A Rab cascade in exocytosisAnother well-characterized Rab cascade is involved in the exocytic transport of secretory vesicles from the trans-Golgi network to the plasma membrane. At the trans-Golgi, the GEF transport protein particle II (TRAPPII) activates the Rab GTPase Ypt32, which then recruits the GEF Sec2 to secretory vesicles. Sec2 in turn activates the Rab Sec4, which binds the Sec15 subunit of the Exocyst tethering complex and allows vesicles to dock and fuse with the plasma membrane (Fig. 3 B; Walch-Solimena et al., 1997; Ortiz et al., 2002; Dong et al., 2007; Itzen et al., 2007). This cascade is conserved in humans. During ciliogenesis at the plasma membrane, the Ypt32 homologue Rab11 recruits the GEF Rabin 8, which in turn activates the human Sec4 homologue Rab8, a process regulated by phosphorylation (Hattula et al., 2002; Wang et al., 2015; Knödler et al., 2010). Interestingly, yeast Sec2 not only is a GEF, but also interacts with the Sec4 effector Sec15 (Medkova et al., 2006), a principle also observed in the endocytic Rab5 activation cycle, where the GEF Rabex5 interacts with the Rab5 effector Rabaptin-5. This dual role may also apply to Mon1-Ccz1, as the Mon1 homologue in C. elegans, SAND1, and yeast Mon1-Ccz1 can bind the HOPS tethering complex (Poteryaev et al., 2010; Nordmann et al., 2010).At the Golgi, phosphatidylinositol-4-phosphate (PI4P) contributes to directionality and spatiotemporal regulation of the exocytic Rab cascade. Sec2 binds both Ypt32 and PI4P on secretory vesicles via two binding sites, a process called coincidence detection. However, PI4P binding inhibits the interaction of Sec2 with Sec15. As vesicles reach the cell periphery, PI4P levels drop by the activity of Osh4, a lipid transporter, which allows Sec2 to bind the Exocyst subunit rather than Ypt32 (Ling et al., 2014; Mizuno-Yamasaki et al., 2010). In addition, Sec2 is phosphorylated by the plasma membrane–localized casein kinases Yck1 and Yck2 (Stalder et al., 2013; Stalder and Novick, 2016), resulting in effector recruitment rather than further Rab activation.Such a regulation may also apply to yeast Mon1-Ccz1. Anionic phospholipids and PI3P support Mon1-Ccz1 recruitment to liposomes and vacuoles (Langemeyer et al., 2020; Cabrera et al., 2014; Lawrence et al., 2014), whereas phosphorylation of the complex by the casein kinase Yck3 inhibits the binding of Mon1-Ccz1 to the Rab5-like Ypt10 and consequently reduces its GEF activity toward Rab7 (Fig. 3 C; Langemeyer et al., 2020). These observations suggest that the phosphorylation of GEFs by kinases may be a general regulatory principle in Rab cascades.Autoinhibition controls the Rab5 GEFAnother widely used regulatory mechanism is the autoinhibition of GEFs to control their activity. This has been analyzed in detail for the early endosomal Rab5-specific GEF Rabex-5, which interacts with the Rab5-effector Rabaptin-5 (Horiuchi et al., 1997). One factor for Rabex-5 recruitment to endocytic vesicles are ubiquitinated cargo proteins at the plasma membrane (Fig. 3 D; Mattera et al., 2006; Lee et al., 2006). Yet, isolated Rabex-5 has only low GEF activity in vitro (Delprato and Lambright, 2007). Structural analysis revealed that binding of Rabaptin-5 to Rabex-5 causes a rearrangement in the Rabex-5 C-terminus, which releases the GEF from autoinhibition and therefore facilitates nucleotide exchange of Rab5 (Delprato and Lambright, 2007; Zhang et al., 2014). On endosomes, increasing amounts of Rab5-GTP further promotes recruitment of the Rabex-5–Rabaptin-5 complex, resulting in a positive feedback loop of Rab5 activation and GEF recruitment (Lippé et al., 2001). Overall, Rabex-5 GEF activity is regulated by autoinhibition, a feedback loop with the Rab5 effector protein Rabaptin-5, and ubiquitinated cargo, which guarantees precise timing in establishing a Rab5-positive endosome. Of note, the Mon1 subunit of the Rab7 GEF can displace Rabex-5 from endosomal membranes (Poteryaev et al., 2010), which suggests a negative feedback loop of the Rab5 activation cascade once the next GEF is present.Regulation of Arf1 GEFs at different Golgi subcompartmentsThese key principles of GEF regulation in GTPase cascades are also found for Arf GTPases. Arf GTPases are soluble in their GDP-bound state by shielding their N-terminal myristate anchor in a hydrophobic pocket. Like Rabs, Arf GTPases are activated by specific GEFs, and their inactivation requires a specific GAP (Sztul et al., 2019). However, this review only highlights some key findings in the regulation of Rab GEFs and does not address regulation of the corresponding GAPs. Once activated, Arfs insert their lipid anchor and an adjacent amphipathic helix into membranes and are then able to bind effector proteins (Sztul et al., 2019). One of the best-studied Arf-GEFs is Sec7, which activates Arf1, an Arf GTPase involved in intra-Golgi trafficking (Achstetter et al., 1988). Studies on yeast Sec7 revealed that the protein is autoinhibited in solution and depends on three small GTPases—Arf1, the Rab Ypt1, and the Arf-like Arl1—for recruitment to the Golgi, a process supported by anionic lipids found in the late Golgi compartment. Importantly, the late Golgi Rabs Ypt31/32 strongly stimulate GEF activity (McDonold and Fromme, 2014; Richardson et al., 2012, 2016), indicating allosteric activation, as observed for Rab5-dependent Mon1-Ccz1 activation (Langemeyer et al., 2020). In this process, Sec7 dimerizes and promotes Arf1 recruitment and thus establishes a positive feedback loop. Interestingly, membrane binding of two additional Arf1 GEFs of the early Golgi, Gea1/2, depends on Rab1/Ypt1 and neutral membranes. Under these conditions, Gea1/2 is released from autoinhibition, although no positive feedback loop was observed (Gustafson and Fromme, 2017). Thus, Arf GEF regulation and Arf activation are tightly linked to multiple small GTPases and the membrane environment to establish Golgi compartments.Regulation and specificity of TRAPP complexes at the GolgiArf1 activation is also linked to the activation of Golgi-specific Rabs. Arf1-GTP binds to the highly conserved TRAPP GEF complexes at the Golgi (Fig. 3 E). Yeast and mammalian cells contain two TRAPP complexes. In yeast, both complexes share seven core components. TRAPPIII in addition contains Trs85, while accessory TRAPPII subunits are instead Trs130, Trs120, Trs65, and Tca17. Metazoan TRAPP complexes contain additional subunits (Lipatova and Segev, 2019).Interestingly, both complexes share the same catalytic site for Rab1/Ypt1 and Rab11/Ypt32. However, TRAPPIII provides GEF activity toward Rab1/Ypt1. Initially, it was proposed that TRAPPII can activate both Rab1/Ypt1 and Rab11/Ypt32 (Thomas et al., 2019, 2018; Thomas and Fromme, 2016; Riedel et al., 2018); however, it was recently shown that the TRAPPII complex is specific for Rab11/Ypt32 (Riedel et al., 2018; Thomas et al., 2019). Reconstitution of GEF activity on liposomes helped here to unravel TRAPP complex substrate specificity, since in solution assays are not adequate to address some of the features important for specific interactions: Rab11/Ypt32 has a longer HVD between the prenyl anchor and the GTPase domain compared with Rab1/Ypt1 (Fig. 3 F, box). The HVD not only binds TRAPPII but also stretches a longer distance from the membrane (Fig. 3 F). Thereby it allows Rab11/Ypt32, but not Rab1/Ypt1, to reach the active site of membrane-bound TRAPPII. Thus, substrate specificity is controlled by the distance of the GTPase domain from the membrane surface, since the active site seems to be located on the opposing site of the complex from the site of membrane interaction (Fig. 3 F; Thomas et al., 2019). The smaller TRAPPIII has its active site closer to the membrane, binds Ypt1 via its shorter HVD, and facilitates its activation, while Ypt32 with its longer HVD may be positioned too far away from the active site. In addition, both complexes require their respective membrane environment for optimal activity, indicating how Arf and Rab GEFs cooperate in Golgi biogenesis.The GEF DENND1 requires Arf5 for Rab35 activationRecently, another example of Arf-mediated Rab activation was reported (Kulasekaran et al., 2021). Rab35, an endocytic Rab found at the plasma membrane and REs (Sato et al., 2008; Kouranti et al., 2006), is involved in cell adhesion and cell migration by controlling the trafficking of β1-integrin and the EGF receptor (Klinkert and Echard, 2016; Allaire et al., 2013). Arf5 binds the Rab35 GEF DENND1 and stimulates its GEF activity, with dysregulation of this cascade linked to glioblastoma growth (Kulasekaran et al., 2021). DENND1 GEF activity is initially autoinhibited and relieved by phosphorylation via the central Akt kinase (Fig. 3 G; Kulasekaran et al., 2015). Similarly, another DENN-domain containing GEF, DENND3, is phosphorylated by the autophagy-specific ULK kinase and then activates Rab12, a small GTPase involved in autophagosome trafficking (Xu et al., 2015). Thus, it seems that Rab GEF activation is more generally linked to other trafficking proteins, such as Arfs, and controlled by kinases and likely also phosphatases.Lessons from reconstitutionOrganelle biogenesis and maintenance in the endomembrane system are tightly linked to the correct spatial and temporal activation of Rab GTPases. A small yeast cell gets by with 11 Rabs, while human cells encode >60 (Hutagalung and Novick, 2011). Rab activation, and therefore membrane identity, of each organelle depends on the cognate GEF. This puts GEFs into the driver’s seat of any Rab-directed function at cellular membranes. It seems that GEFs integrate, by several regulatory loops, incoming signals from various sources such as membrane composition, cargo proteins, upstream GTPases, or kinases/phosphatases (Fig. 3 A). Yet our insights on the specific membrane targeting and regulation of GEFs remain incomplete for want of available experimental approaches. We briefly discuss here how recent advances on the reconstitution of GEF-mediated Rab activation at model membranes have advanced our understanding of organelle maturation and biogenesis.Reconstitution of any reaction to uncover the essential constituents is limited by the available tools. GEFs, Rabs, Sec18/Munc1 proteins, tethering factors, and SNAREs are for instance required for membrane fusion (Fig. 3 A). Initial assays focused on SNAREs and revealed their important but rather inefficient fusogenicity (Weber et al., 1998). Further analyses uncovered critical activation steps for SNAREs (Malsam et al., 2012; Pobbati et al., 2006; Südhof and Rothman, 2009; Jahn and Scheller, 2006), yet fusion at physiological SNARE concentrations in various in vitro systems does not occur, unless assisted by chaperoning Sec1/Munc18 proteins and tethering factors (Bharat et al., 2014; Lai et al., 2017; Mima and Wickner, 2009; Ohya et al., 2009; Wickner and Rizo, 2017). Most tethers again depend on Rabs for their localization, and Rab localization to membranes requires a GEF (Cabrera and Ungermann, 2013), whose activity can be a limiting factor for fusion (Langemeyer et al., 2020, 2018b). The long avenue of understanding the mechanism and regulation of membrane fusion exemplifies the challenges in dissecting the complexity of a cellular reaction, but also demonstrates the powerful insights obtained from reconstitution of these processes.GEFs determine the localization of the corresponding Rab, and consequently, Rabs follow their GEF if they are mistargeted (Gerondopoulos et al., 2012; Blümer et al., 2013; Cabrera and Ungermann, 2013). However, these anchor-away approaches completely bypass the tight cellular regulation of GEF activation by the mistargeting and additional overexpression of the GEF protein and may allow only statements about GEF/substrate specificity. The spatiotemporal activation of each GEF at the right organelle is vital for the timing of all downstream reactions. GEFs are recruited to membranes by coincidence detection, which includes membrane lipids such as PIPs, membrane packaging defects, and peripheral membrane proteins such as upstream Rabs or other small GTPases. This recruitment is often accompanied by the release from autoinhibition, which may be triggered or inhibited by other regulatory processes such as phosphorylation. It comes as no surprise that pathogens such as Legionella and Salmonella take advantage of the central function of GEFs to establish and nourish their intracellular organellar niche by manipulating small GTPase activity (Spanò and Galán, 2018).To understand the specificity of Rab GEFs (and GAPs), mostly very simplified systems were used. Most GEF assays analyze soluble Rabs loaded with fluorescent 2′-O-(N-methylanthraniloyl) (MANT)-nucleotide or radioactively labeled GTP/GDP and soluble GEF in a test tube, where nucleotide exchange activity is observed upon addition of unlabeled nucleotide (Fig. 4 A). This strategy allows the identification of substrate (Rab) specificity of GEFs, but could also lead to misleading results, as pointed out earlier on the example of the TRAPP complexes and Rab1/Ypt1 or Rab11/Ypt32. In addition, GEF-Rab pairs negatively regulated by one of the above principles could easily be missed.Open in a separate windowFigure 4.Approaches to determine GEF activity in vitro. Methods to determine GEF activity for Mon1-Ccz1. In all approaches, Rab7 is preloaded with fluorescent MANT-GDP. Fluorescence decreases upon GEF-mediated nucleotide exchange. (A) GEF assays. (Ai) In-solution Rab GEF assay. Mon1-Ccz1 (blue, Bulli/Rmc1/C18orf8 subunit, indicated by unlabeled hexagon) and Rab7 (gray) are freely diffusible in the test tube, which results in random collision and Rab activation. (Aii) GEF-mediated activation of artificially recruited Rab7 on liposomes. Rab7 with a C-terminal 6xHis-tag is permanently immobilized on membranes containing the cationic lipid DOGS-NTA. Mon1-Ccz1 unspecifically binds to this membrane surface and activates Rab7. Diffusion is limited to the membrane surface, thus increasing chances of interactions. (Aiii) Reconstitution of Rab5-mediated Rab7 activation by Mon1-Ccz1 on liposomes. Chemically activated, prenylated Rab5 (green), delivered to the membrane by the Rab Escort Protein (REP), allows Mon1-Ccz1 recruitment and Rab7 activation from the GDI complex (see text for further details). (B) Summary of Ai–Aiii. pren., prenylation.As Rabs and GEFs function on membranes, we and others adopted strategies for measuring Rab activation by GEFs on membranes (Fig. 4 B). In a first approach, Rab and other small GTPases (Sot et al., 2013; Schmitt et al., 1994) were immobilized with C-terminal hexahistidine tags on liposomes containing the polycationic lipid 1,2-dioleoyl-sn-glycero-3-[(N-(5-amino-1-carboxypentyl)iminodiacetic acid)succinyl] (DOGS-NTA) and observed higher activity of the added GEF (Cabrera et al., 2014; Thomas and Fromme, 2016). A drawback of this technique is the artificial membrane composition. To avoid potential artifacts of unnaturally charged membranes and permanently membrane-bound Rab, recent studies relied on prenylated Rabs in complex with GDI. Reflecting the natural source of the cytoplasmic Rab pool, this complex was used as a GEF substrate in the presence of liposomes mimicking the natural membrane composition (Cezanne et al., 2020; Bezeljak et al., 2020; Langemeyer et al., 2020, 2018b; Thomas et al., 2018, 2019; Thomas and Fromme, 2016).Even though these observations are recent, the outcome and the understanding of GEF regulation is encouraging. For the Rab5 GEF complex consisting of Rabex5 and Rabaptin5, GEF-dependent Rab5 recruitment to membranes revealed a self-organizing system, nonlinear Rab5 patterning, and collective switching of the Rab5 population (Bezeljak et al., 2020; Cezanne et al., 2020). This is in agreement with mathematical modeling and predictions on bistability and ultrasensitivity of Rab networks (Del Conte-Zerial et al., 2008; Barr, 2013). For the Golgi-resident TRAPPII and TRAPPIII complexes, the membrane composition, the length of the Rab HVD, and the presence of membrane-bound Arf1 determined the GEF specificity for their Rabs (Fig. 3 F; Thomas et al., 2019, 2018; Thomas and Fromme, 2016; Riedel et al., 2018), which is nicely supported by recent structural analyses of yeast and metazoan TRAPPIII (Galindo et al., 2021; Joiner et al., 2021)Our own data uncovered that the yeast and metazoan Mon1-Ccz1(-RMC1) complex required membrane-bound Rab5-GTP to activate Rab7 out of the GDI complex (Langemeyer et al., 2020). Surprisingly, Rab5-GTP not only determined membrane binding of Mon1-Ccz1, but also activated the GEF on membranes by a yet-unknown mechanism (Fig. 1 C). Phosphorylation of yeast Mon1-Ccz1 by the casein kinase Yck3 inhibited this activation, demonstrating possible regulation of GEF activity (Fig. 3 C). Importantly, this finding agrees with the observed Rab5-to-Rab7 switch in vivo (Poteryaev et al., 2010; Rink et al., 2005).Taken together, the available tools open exciting avenues for our understanding of organelle maturation. Reconstitution will allow the investigation of an entire Rab cascade and its regulation by kinases or membrane lipids. It will be possible to determine the cross-talk with lipid kinases and observe possible regulatory loops between Rabs and PI kinases (Tremel et al., 2021). We are confident that such analyses, complemented by in vivo analyses of Rabs or other small GTPases and their GEFs, will clarify the underlying mechanism of organelle maturation and biogenesis along the endomembrane system of eukaryotic cells.     

Functional Separation of Endosomal Fusion Factors and the Class C Core Vacuole/Endosome Tethering (CORVET) Complex in Endosome Biogenesis

Transport along the endolysosomal system requires multiple fusion events at early and late endosomes. Deletion of several endosomal fusion factors, including the Vac1 tether and the Class C core vacuole/endosome tethering (CORVET) complex-specific subunits Vps3 and Vps8, results in a class D vps phenotype. As these mutants have an apparently similar defect in endosomal transport, we asked whether CORVET and Vac1 could still act in distinct tethering reactions. Our data reveal that CORVET mutants can be rescued by Vac1 overexpression in the endocytic pathway but not in CPY or Cps1 sorting to the vacuole. Moreover, when we compared the ultrastructure, CORVET mutants were most similar to deletions of the Rab Vps21 and its guanine nucleotide exchange factor Vps9 and different from vac1 deletion, indicating separate functions. Likewise, CORVET still localized to endosomes even in the absence of Vac1, whereas Vac1 localization became diffuse in CORVET mutants. Importantly, CORVET localization requires the Rab5 homologs Vps21 and Ypt52, whereas Vac1 localization is strictly Vps21-dependent. In this context, we also uncover that Muk1 can compensate for loss of Vps9 in CORVET localization, indicating that two Rab5 guanine nucleotide exchange factors operate in the endocytic pathway. Overall, our study reveals a unique role of CORVET in the sorting of biosynthetic cargo to the vacuole/lysosome.     

The yeast vacuolar Rab GTPase Ypt7p has an activity beyond membrane recruitment of the homotypic fusion and protein sorting-Class C Vps complex

A previous report described lipid mixing of reconstituted proteoliposomes made using lipid mixtures that mimic the composition of yeast vacuoles. This lipid mixing required SNARE {SNAP [soluble NSF (N-ethylmaleimide-sensitive factor)-attachment protein] receptor} proteins, Sec18p and Sec17p (yeast NSF and α-SNAP) and the HOPS (homotypic fusion and protein sorting)-Class C Vps (vacuole protein sorting) complex, but not the vacuolar Rab GTPase Ypt7p. The present study investigates the activity of Ypt7p in proteoliposome lipid mixing. Ypt7p is required for the lipid mixing of proteoliposomes lacking cardiolipin [1,3-bis-(sn-3'-phosphatidyl)-sn-glycerol]. Omission of other lipids with negatively charged and/or small head groups does not cause Ypt7p dependence for lipid mixing. Yeast vacuoles made from strains disrupted for CRD1 (cardiolipin synthase) fuse to the same extent as vacuoles from strains with functional CRD1. Disruption of CRD1 does not alter dependence on Rab GTPases for vacuole fusion. It has been proposed that the recruitment of the HOPS complex to membranes is the main function of Ypt7p. However, Ypt7p is still required for lipid mixing even when the concentration of HOPS complex in lipid-mixing reactions is adjusted such that cardiolipin-free proteoliposomes with or without Ypt7p bind to equal amounts of HOPS. Ypt7p therefore must stimulate membrane fusion by a mechanism that is in addition to recruitment of HOPS to the membrane. This is the first demonstration of such a stimulatory activity--that is, beyond bulk effector recruitment--for a Rab GTPase.     

The CORVET Subunit Vps8 Cooperates with the Rab5 Homolog Vps21 to Induce Clustering of Late Endosomal Compartments

Membrane tethering, the process of mediating the first contact between membranes destined for fusion, requires specialized multisubunit protein complexes and Rab GTPases. In the yeast endolysosomal system, the hexameric HOPS tethering complex cooperates with the Rab7 homolog Ypt7 to promote homotypic fusion at the vacuole, whereas the recently identified homologous CORVET complex acts at the level of late endosomes. Here, we have further functionally characterized the CORVET-specific subunit Vps8 and its relationship to the remaining subunits using an in vivo approach that allows the monitoring of late endosome biogenesis. In particular, our results indicate that Vps8 interacts and cooperates with the activated Rab5 homolog Vps21 to induce the clustering of late endosomal membranes, indicating that Vps8 is the effector subunit of the CORVET complex. This clustering, however, requires Vps3, Vps16, and Vps33 but not the remaining CORVET subunits. These data thus suggest that the CORVET complex is built of subunits with distinct activities and potentially, their sequential assembly could regulate tethering and successive fusion at the late endosomes.