Abstract
Lysosome-related organelles (LROs) comprise a group of cell type-specific subcellular compartments with unique composition, morphology and structure that share some features with endosomes and lysosomes and that function in varied processes such as pigmentation, hemostasis, lung plasticity and immunity. In recent years, studies of genetic diseases in which LRO functions are compromised have provided new insights into the mechanisms of LRO biogenesis and the regulated secretion of LRO contents. These insights have revealed previously unappreciated specialized endosomal sorting processes in all cell types, and are expanding our views of the plasticity of the endosomal and secretory systems in adapting to cell type-specific needs.
Introduction
The endocytic pathway fulfills many important functions in all cells, but additional adaptations of the endosomal system in specialized metazoan cell types underlie the formation of lysosome-related organelles (LROs). LROs comprise a group of functionally diverse compartments that share features with lysosomes but are distinct and harbor specific cargoes that confer their unique properties [1]. Consistent with their distinct functions, LROs vary in composition and morphology, ranging from pleiomorphic secretory granules in platelets, cytotoxic T lymphocytes (CTLs) and other hematopoietic cells to enormous fluid-filled vacuoles in the vertebrate notochord and complex subcompartmentalized structures such as pigment cell melanosomes, endothelial cell Weibel-Palade bodies, or platelet α granules. Maturing phagosomes in phagocytes such as dendritic cells, neutrophils and macrophages receive unique contents from endosomes, and thus can also be considered “inducible” LROs. LROs are diverse not only in morphology, but also in the origin of their membranes, the derivation of their contents from secretory and endosomal sources, and the complement of machineries exploited for their formation, maturation and secretion. Here we highlight recent advances in our understanding of these properties, focusing on a few areas that hold particular promise for future breakthroughs.
LRO biogenesis: Origin of LRO precursors
All LROs progressively mature from precursors by acquiring specialized cargoes and generating a lumenal environment conducive for their function (Figure 1). However, the origin of the precursor differs, as exemplified by four well-studied LROs – pigment cell melanosomes, endothelial cell Weibel Palade Bodies (WPBs), platelet α granules and CTL and natural killer (NK) cell lytic granules (LGs) (Figure 2). Non-pigmented melanosome precursors, or premelanosomes, develop from intermediate compartments with features of early endosomal vacuolar domains with few intraluminal vesicles (ILVs) and extended bilayered cytosolic coats [2]. The ILVs scaffold the polymerization of amyloid fibrils by the pigment cell-specific protein PMEL [3]; the fibrils assemble into sheets that distend the organelle into an ellipsoidal shape [2] and template melanin deposition [3]. Accordingly, pigment cells in Pmel−/− mice accumulate melanin in round melanosomes that lack characteristic striations, but that nevertheless remain segregated from the endolysosomal system [4]. Immature WPBs emerge from the trans Golgi Network (TGN) as von Willebrand Factor (vWF) assembles into tubules that shape the nascent compartment into a cigar-shaped organelle [5]. Platelet α granules derive from late endosomes/ multivesicular endosomes (MVEs) in megakaryocytes, and harbor both biosynthetic (e.g. vWF) and endocytic (e.g. fibrinogen) contents. Mature α granules retain CD63 on ILVs as they segregate from endosomes [6]. Whereas matured melanosomes, WPBs and α granules coexist with classical lysosomes, LGs are likely modified lysosomes with a ring of ILVs surrounding a dense core [7] that further mature upon T cell activation. The dense cores might derive like conventional secretory granules from the TGN and later fuse with MVEs to form a hybrid organelle (Figure 1).
Melanosomes and WPBs as model LROs
LROs such as LGs and platelet dense granules lack well-organized structural scaffolds, but WPBs and melanosomes develop around rigid matrices.
PMEL is an integral membrane protein that is proteolytically processed into (i) a luminally-exposed amyloidogenic domain that generates the melanosomal fibrils, and (ii) integral membrane fragments that are eventually degraded [3]. Association of the PMEL luminal domain with ILVs requires the tetraspanin (TSP) CD63, but – unlike for most known ILV cargoes – not ubiquitylation or ESCRT function [8,9••]. CD63 is also required for the sorting and proteolytic maturation of elastase – a component of primary granules in neutrophils [10] – suggesting that TSPs on endosomes might generally function to retain proteins that are destined for LROs and prevent them from ESCRT-dependent degradation. This might explain why CD63 associates with most LROs despite associating with late endosomes/ lysosomes in cells that lack LROs [11]. In melanocytes, the integral membrane PMEL fragments are degraded in an ubiquitin- and ESCRT-dependent manner [9••], thus illustrating independent sorting mechanisms for different topological domains of the same protein.
The tubular vWF structures that assemble at the TGN during WPB biogenesis differ substantially from the PMEL amyloid fibrils. Electron tomography identified the vWF tubules as regularly-spaced helical structures [12–14]. The vWF helices likely aggregate to form a paracrystalline core in the TGN [14], causing retention and ultimate segregation into distinct membrane structures that retain cargoes such as P-selectin or insulin growth factor binding protein-7 (IGFBP7) [15]. Interestingly, vWF in platelet α granules forms shorter tubules that typically accumulate around a central core of heterogeneous, electron dense material (Figure 2), and are not responsible for the tubular shape of α granules [6].
LRO biogenesis: Precursor maturation
Whether they originate from endosomal or TGN membranes (Figure 1), LRO precursors mature by acquiring key transmembrane components – such as melanogenic enzymes in melanosomes or serotonin and calcium transporters in platelet dense granules – via membrane trafficking. Maturation also provides a means to acquire effectors that are required for LRO motility or secretion (Figure 1). LROs mature via an intimate dialogue between the immature organelle and MVEs and/or specialized domains of early sorting and recycling endosomes, ensuring that critical cargoes are diverted from classical endo-lysosomes and toward maturing LROs. Multiple non-redundant pathways generally deliver distinct transmembrane protein cargoes to the same maturing LRO, as exemplified by cargo acquisition from the TGN and early endosomes during WPB maturation, and from distinct early endosomal domains during melanosome maturation (Figure 1). The use of multiple pathways ensures that critical complex functions – such as the onset of melanin synthesis by convergence of the copper-dependent Tyrosinase enzyme with the copper transporter ATP7A [16] – are only observed in the mature organelle.
Hermansky-Pudlak syndrome and cargo delivery
Hermansky-Pudlak syndrome (HPS) and its mouse models comprise a group of genetic disorders characterized by malformation of melanosomes, platelet dense granules, and in some cases other LROs [17]. The affected genes encode subunits of five cytoplasmic multisubunit protein complexes – adaptor protein (AP)-3, vacuolar protein sorting (VPS)-C, and biogenesis of lysosome-related organelles complex (BLOC)-1, -2 and -3 [17] – that impact membrane trafficking and/or protein sorting to facilitate LRO maturation. The complexes are ubiquitously expressed, but altered expression levels, post-translational modifications, and/or unique interactions with trafficking machinery in LRO-containing cell types support their functions in critical non-redundant trafficking pathways. For these reasons, their loss of function preferentially impacts LRO maturation.
AP-3 and VPS-C
AP-3 is a heterotetrameric adaptor that engages transmembrane cargoes via cytoplasmic sorting signals in early endosomes, and packages them into clathrin-coated transport vesicles [18]. AP-3 is required for the biogenesis of eye pigment granules in Drosophila melanogaster and gut granules in Caenorhabditis elegans, and for delivery of multiple cargoes to vertebrate LROs [18] (Figure 1), including OCA2 to melanosomes [19,20], CD63 to WPBs [21], toll-like receptor 9 (TLR9) to an IRF7-signaling LRO in plasmacytoid dendritic cells [22], TLR4 to phagosomes in conventional dendritic cells [23•], and SLC35D3 likely to dense granules in platelets [24]. The heterotetrameric VPS-C core (containing VPS11, 16, 18 and 33) assembles into two larger complexes in the yeast Saccharomyces cerevisiae, HOPS and CORVET [25]. VPS-C/ HOPS in S. cerevisiae, D. melanogaster and vertebrates regulates tethering and SNARE-dependent fusion within the endosomal system [26,27], including of AP-3-coated vesicles with the lysosome-like vacuole [28]. Metazoans express distinct VPS-C complexes containing alternative VPS33 and VPS16-like isoforms. The mouse Vps33a buff mutation impacts melanosome and platelet dense granule maturation [29] and mutations in D. melanogaster VPS33A or VPS16A cause defects in eye pigment granules [30]. By contrast, mutations in VPS33B or the VPS16-like VIPAS39 underlie Arthrogryposis-Renal dysfunction-Cholestasis (ARC) syndrome [31,32] characterized by a loss of platelet α granules among other system defects [33,34].
BLOC-1
The eight subunits of BLOC-1 lack recognizable functional domains, and the molecular functions of the complex are not known. In melanocytes, BLOC-1 localizes to endosomal tubules [35] and is required to export melanosomal cargoes from vacuolar early endosomes [16,36,37] into recycling endosome-derived tubular carriers that fuse with melanosomes [38]. However, BLOC-1 unlikely functions as a sorting adaptor, as its architecture – a linear chain of eight globular domains [39•] – is unlike other adaptors, and direct interactions between BLOC-1 and cargoes have not been observed. BLOC-1 binds in vitro to endosomal Q SNAREs Syntaxin 13 and SNAP-25 [40], and might either sort them into transport carriers or regulate their interaction with a partner R-SNARE. A recent proteomics analysis identified tethering factors and two members of the peroxiredoxin family of oxidoreductases as additional binding partners [41].
AP-3 and BLOC-1 physically interact [35] and coordinately regulate cargo distribution in neurons [42,43]. However, in melanocytes BLOC-1 and AP-3 localize distinctly on early endosomes to tubular domains and buds, respectively, [35,36], and BLOC-1 functions in cargo transport to melanosomes either independently of AP-3 (as for ATP7A and the melanogenic enzyme TYRP1 [16,36]) or in conjunction with AP-3 (as for the transporter OCA2 [20]). Similarly, BLOC-1 regulates transport of cargoes that are both AP-3-dependent and independent to gut granules in C. elegans [44•]. This suggests that BLOC-1 acts in conjunction with sorting adaptors to effect cargo transport.
BLOC-2, BLOC-3, RAB32 and RAB38
The two-subunit BLOC-3 is a guanine nucleotide exchange factor (GEF) for two tissue-specific Rab GTPases, RAB38 and RAB32 [45••], that regulate cargo delivery to nascent melanosomes [46,47], platelet dense granules [48], lamellar bodies [49,50], and notochord vacuoles [51••]. How these two partially redundant small GTPases function is not clear. When bound to GTP, both interact with AP-3, the heterotetrameric BLOC-2 – which functions downstream of BLOC-1 in cargo transport [35,36,52] – and the heterotetrameric adaptor AP-1 [53]. They also both bind to VARP [54], a putative scaffold that engages and maintains the R-SNARE VAMP7/TI-VAMP in an inactive conformation [55,56••]. This suggests that RAB32 and RAB38, through multiple effectors, integrate cargo sorting into transport carriers and fusion of the carriers with target LROs. The latter would be consistent with the localization of a cohort of endogenous or overexpressed epitope tagged-RAB32 and/or -RAB38 to LROs [45••,46,48,50,51,53]. RAB32 and RAB38 activation is under complex regulation. VARP is a GEF for the early endosomal Rab GTPase, RAB21 [57], and BLOC-3 is an effector of RAB9 [58], implying that RAB32 and RAB38 participate in several Rab cascades during LRO maturation. Moreover, the existence of GEFs for RAB38 orthologues in C. elegans [59] and D. melanogaster [60] that are unrelated to BLOC-3 suggests that additional GEFs might exist in mammals, perhaps explaining why melanosome biogenesis is differentially affected by loss of BLOC-3 function in different pigment cell types [61].
Other components of the biogenesis machinery
LYST and NBEAL2
Mutations in two members of a family of large proteins with a conserved BEACH domain cause LRO biogenesis disorders. Mutations in LYST/ CHS1 underlie Chediak-Higashi syndrome, in which many LROs and conventional lysosomes are grossly enlarged, but the molecular function of this 3801-residue protein is unclear. The orthologous lvsB controls cargo transport from lysosomes to an LRO in Dictyostelium discoideum [62], perhaps by antagonizing RAB14-dependent fusion between lysosomes and LROs [63]. Alternatively, LYST might promote lysosome or LRO fission, as it does in macrophages [64]. Mutations in another BEACH protein, NBEAL2, underlie Gray Platelet Syndrome, characterized by an absence of platelet α granules [65–67•]. How NBEAL2 functions is unclear, but a role in fission of α granule contents from MVBs would parallel the proposed function of LYST in macrophages.
AP-1 and motors
A second ubiquitous heterotetrameric adaptor family member – AP-1 – plays an important but varied role in LRO generation. In melanocytes, AP-1 binds to targeting signals in several melanosome cargoes, [20,38,68,69] and is required for delivery of TYRP1 to mature melanosomes [38]. However, it is not clear whether the cargo sorting function of AP-1 is required. AP-1 on endosomal buds binds to the microtubule plus end-directed kinesin motor, KIF13A, promoting the extension of tubular Rab11-positive recycling endosomes to the cell periphery. This apposes the endosomes to maturing melanosomes, facilitating cargo delivery via the tubular transport carriers [38]. AP-1 also binds to TSG101, an ESCRT-I subunit involved in MVB formation [70] that is also required in TYRP1 delivery to melanosomes [71]. In endothelial cells, AP-1 and clathrin function as a scaffold to maintain the compacted, cigar-like structure of WPBs which is necessary for positioning vWF polymers to “unfurl” upon WPB secretion and for consequent platelet adhesion to the endothelial cell [5]. AP-1 plays a secondary role in facilitating WPB secretion through recruitment of its cofactors, amphiphilin and γ-synergin [72]. Platelet α granules are also bordered by clathrin lattices [6], but whether they contribute to α granule morphogenesis is not known.
Cytoskeletal motors have important roles in LRO motility and secretion (see below), but unconventional myosins function in LRO biogenesis likely by effecting actin rearrangements that facilitate membrane dynamics involved in budding and fusion. For example, in melanocytes, myosin VI – an actin-based motor involved in endocytic recycling – recruits actin to mature melanosomes and regulates melanosome size and melanization [73].
LRO secretion: polarization and docking
Most, if not all, LROs release their lumenal contents by secretion into the extracellular space or directly to neighbouring cells in response to signaling. This requires LRO transport to the cell periphery and stimulus-dependent fusion of the LRO and plasma membranes.
In endothelial cells, mature WPBs appear “ready” to release vWF – with the assistance of actin/ myosin II-based contractile forces – upon stimulation [74••]. Similarly, in resting platelets, fully matured α granules, dense granules and lysosomes are primed for stimulus-dependent fusion, but the kinetics of their release differ. Dense granules are likely docked at the plasma membrane and released immediately upon stimulus [75•], whereas content release from α granules is more heterogeneous and slightly delayed [75•,76]; the heterogeneity might reflect packaging into distinct α granule subsets [76,77] or spatial segregation within internally heterogeneous α granules [6]. Unlike platelet granules and WPBs, LGs in resting CTLs are functionally immature. Final maturation and fusion are triggered by target cell engagement, inducing the fusion of LGs with RAB11-containing compartments [78] (Figure 1) that deliver effectors required for positioning, fusion with the plasma membrane or both.
Genes mutated in Griscelli syndrome (GS) encode essential components of the molecular machinery that allow for LRO docking at the cell periphery. In melanocytes, RAB27A (GS1), myosin VA (GS2) and melanophilin (GS3) form a complex that tether melanosomes to cortical actin, permitting their ultimate transfer from dendritic tips to keratinocytes (reviewed in [79]). WPB and LG secretion also require RAB27A at multiple steps, but the effectors are distinct from those on melanosomes. WPB secretion requires coordination of RAB27A, RAB15, and their effector MUNC13-4 with RAB3 [80], and is regulated by a balance between RAB27A availability, Slp4-a as a stimulating effector, and MyRIP as an inhibitory effector [81•]. In CTLs, a complex of the RAB27A effector Slp3 with kinesin-1 drives LGs to the plasma membrane for ultimate secretion [82•]. RAB27A and MUNC13-4 play independent roles in stimulus-induced LG maturation [78], but a Rab27A-MUNC13-4 complex is subsequently required to tether LGs to the plasma membrane for secretion [83•].
Stimulus-dependent LG secretion in CTLs and NK cells is under tight control to ensure that lumenal cytolytic contents are directed only toward a target cell at the immunological synapse. LGs polarize toward the synapse in association with the centrosome, which is repositioned toward the plasma membrane upon target cell contact [84,85••]. Centrosome motility is tightly controlled by the strength of T cell signaling [86], at least in part via activation of the Lck tyrosine kinase [86], and requires the minus end-directed microtubule motor dynein [84,87]. Apposition of LGs to the plasma membrane further requires actin rearrangements [84,88]. A similar mode of centrosome positioning and docking targets MHC class II compartments to the immunological synapse of B lymphocytes [89].
LRO secretion: FHL and the fusion apparatus
Familial hemophagocytic lymphohistiocytosis (FHL) is a genetic disorder characterized by unchecked lymphocyte expansion and inflammation due to impaired LG function in CTLs and NK cells [90]. FHL types 3–5, which are additionally associated with bleeding diathesis, reflect impaired LG and platelet granule release. FHL4 results from gene mutations in the Qa SNARE Syntaxin 11 (STX11). FHL4 CTLs and NK cells do not undergo target cell-induced LG degranulation [91,92], and STX11-deficient platelets fail to secrete α granule and dense granule contents in response to agonists [93]. This implies that a STX11-containing tSNARE mediates a fusion step required for LRO release. FHL5 results from mutations in STXBP2 encoding the Sec1-Munc18 family member, Munc18-2/ Munc18b [94]. Munc18b binds to and stabilizes STX11 and facilitates SNARE complex formation; accordingly, FHL4 and FHL5 CTLs and platelets show similar degranulation defects [93–95••]. In platelets STX11 and Munc18b complex with the Qbc SNARE SNAP-23 on the plasma membrane and the R-SNARE VAMP8 on granule membranes to mediate fusion and granule content release [93,95••]. A similar SNARE complex likely functions during LG degranulation in CTLs and NK cells, but where the complex forms in these cells is less clear. STX11 localizes in CTLs and NK cells primarily to intracellular structures that lack RAB27A [92,96] and that might be identical to the RAB11-containing compartments that fuse with immature LGs upon CTL stimulation [78]. This fusion step in CTLs requires the RAB27A effector MUNC13-4 [78]. MUNC13-4 is a SNARE interacting protein that is mutated in FHL3, is required for degranulation of LGs [97] and platelet granules [98], and forms a complex with STX11 and Munc18b in platelets [95••]. Together, the data suggest that whereas STX11/Munc18b/MUNC13-4-dependent SNARE complex formation directly mediates degranulation in platelets, it may mediate a preparatory maturation step in CTLs and NK cells.
Perspectives
While our understanding of LRO biogenesis and secretion has deepened considerably in recent years, many questions remain and will likely be the focus of study in coming years. Firstly, how do LRO precursors such as premelanosomes and α granules segregate from the endosomal system? In both cases, both LROs and lysosomes emerge from common MVEs, and segregation appears to be independent of structural rigidity imposed by vWF or PMEL. Differential sorting of distinct cargo domains into separate ILVs might reflect a general feature of LRO precursors. Secondly, how is cargo assembly differentially regulated in distinct LRO-producing cells? For example, vWF polymerizes into elongated tubules in endothelial cell WPBs but into shorter tubules in α granules. Third, while we have amassed a reasonable “parts” list for both LRO maturation and the docking and fusion apparatus for secretion, the mechanisms by which these parts are integrated to effect their function is not yet understood. Understanding these mechanisms will require a combination of systems analyses, biochemical analyses of binding interactions among machinery components, and functional analyses of model cell types expressing targeted mutations that disrupt component interactions. Finally, comparative analyses between LRO-generating cell types will likely provide novel insights into common and distinctive features of LROs. For example, FHL is not characterized by hypopigmentation, and thus melanin transfer to keratinocytes is not likely mediated by the same fusion complex employed by platelets or CTLs to secrete their granules; indeed, a recent study suggests that melanocytes release melanosome clusters in dendritic tips by abscission of the plasma membrane in regions of adherence to keratinocytes [99]. Validation and molecular dissection of this mechanism might reveal novel ways in which LRO contents are released.
Acknowledgments
We thank our many colleagues who have contributed to the work described herein, particularly Ilse Hurbain and Maryse Romao for contributing figures, and apologize to those whose work we failed to cite. We are grateful for funding from the National Institutes of Health (grants R01 AR048155, R01 EY015625, R21 HL096865 and R21 AI092398), Netherlands Organisation for Scientific Research (grant ALW 813.08.001), Institut Curie, CNRS, INSERM, and Fondation ARC pour la recherche sur le cancer (grant SL220100601359). The funding sources had no involvement in the preparation or submission of this work.
Footnotes
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