Peroxin-dependent targeting of a lipid-droplet-destined membrane protein to ER subdomains

MIGA2 Links Mitochondria, the ER, and Lipid Droplets and Promotes De Novo Lipogenesis in Adipocytes

Physical contact between organelles is vital to the function of eukaryotic cells. Lipid droplets (LDs) are dynamic organelles specialized in lipid storage that interact physically with mitochondria in several cell types. The mechanisms coupling these organelles are, however, poorly understood, and the cell-biological function of their interaction remains largely unknown. Here, we discover in adipocytes that the outer mitochondrial membrane protein MIGA2 links mitochondria to LDs. We identify an amphipathic LD-targeting motif and reveal that MIGA2 binds to the membrane proteins VAP-A or VAP-B in the endoplasmic reticulum (ER). We find that in adipocytes MIGA2 is involved in promoting triglyceride (TAG) synthesis from non-lipid precursors. Our data indicate that MIGA2 links reactions of de novo lipogenesis in mitochondria to TAG production in the ER, thereby facilitating efficient lipid storage in LDs. Based on its presence in many tissues, MIGA2 is likely critical for lipid and energy homeostasis in a wide spectrum of cell types.

Parkin-mediated ubiquitylation redistributes MITOL/March5 from mitochondria to peroxisomes

Ubiquitylation of outer mitochondrial membrane (OMM) proteins is closely related to the onset of familial Parkinson's disease. Typically, a reduction in the mitochondrial membrane potential results in Parkin‐mediated ubiquitylation of OMM proteins, which are then targeted for proteasomal and mitophagic degradation. The role of ubiquitylation of OMM proteins with non‐degradative fates, however, remains poorly understood. In this study, we find that the mitochondrial E3 ubiquitin ligase MITOL/March5 translocates from depolarized mitochondria to peroxisomes following mitophagy stimulation. This unusual redistribution is mediated by peroxins (peroxisomal biogenesis factors) Pex3/16 and requires the E3 ligase activity of Parkin, which ubiquitylates K268 in the MITOL C‐terminus, essential for p97/VCP‐dependent mitochondrial extraction of MITOL. These findings imply that ubiquitylation directs peroxisomal translocation of MITOL upon mitophagy stimulation and reveal a novel role for ubiquitin as a sorting signal that allows certain specialized proteins to escape from damaged mitochondria.

Lipid Droplet and Peroxisome Biogenesis: Do They Go Hand-in-Hand?

All eukaryotic cells contain membrane bound structures called organelles. Each organelle has specific composition and function. Some of the organelles are generated de novo in a cell. The endoplasmic reticulum (ER) is a major contributor of proteins and membranes for most of the organelles. In this mini review, we discuss de novo biogenesis of two such organelles, peroxisomes and lipid droplets (LDs), that are formed in the ER membrane. LDs and peroxisomes are highly conserved ubiquitously present membrane-bound organelles. Both these organelles play vital roles in lipid metabolism and human health. Here, we discuss the current understanding of de novo biogenesis of LDs and peroxisomes, recent advances on how biogenesis of both the organelles might be linked, physical interaction between LDs and peroxisomes and other organelles, and their physiological importance.

Lipid droplet biogenesis

Lipid droplets (LDs) store neutral lipids in their core as an energy source when nutrients are scarce. The center of an LD is hydrophobic, and hence it is surrounded by a phospholipid monolayer, unlike other organelles that have an aqueous interior and are bounded by a phospholipid bilayer. LDs arise from the ER, where neutral lipid synthesis enzymes are localized. A combination of biophysical analysis and modeling, in vitro reconstitution and cell biological analyses has provided a great deal of information over the past few years on the process of LD biogenesis from the ER. In addition to lipid composition, four protein families (seipin proteins, perilipins, FIT proteins and ER shaping proteins) are crucial for LD biogenesis. Recent studies have shown that LDs preferentially arise, along with peroxisomes, at special ER sites marked by the reticulon-like Pex30/MCTP2 protein. New functions for perilipins and FIT family proteins have been uncovered, and the cryo-electron microscopy structure of seipin coupled with high resolution imaging in cells has provided a more comprehensive picture of its function in LD biogenesis. Seipin, along with other proteins such as Rab18 and its effector NRZ, have been shown to carry out their functions at least in part through regulation of ER-LD contact sites, whose establishment and maintenance have emerged as an essential component of LD biogenesis and maturation.

Born this way - Biogenesis of lipid droplets from specialized ER subdomains

Both the endoplasmic reticulum (ER) and lipid droplets (LDs) are key players in lipid handling. In addition to this functional connection, the two organelles are also tightly linked due to the fact that the ER is the birthplace of LDs. LDs have an atypical architecture, consisting of a neutral lipid core that is covered by a phospholipid monolayer. LD biogenesis starts with neutral lipid synthesis in the ER membrane and formation of small neutral lipid lenses between its leaflets, followed by budding of mature LDs toward the cytosol. Several ER proteins have been identified that are required for efficient LD formation, among them seipin, Pex30, and FIT2. Recent evidence indicates that these LD biogenesis factors might cooperate with specific lipids, thus generating ER subdomains optimized for LD assembly. Intriguingly, LD biogenesis reacts dynamically to nutrient stress, resulting in a spatial reorganization of LD formation in the ER.

Intracellular communication between lipid droplets and peroxisomes: the Janus face of PEX19

In order to adapt to environmental changes, such as nutrient availability, cells have to orchestrate multiple metabolic pathways, which are catalyzed in distinct specialized organelles. Lipid droplets (LDs) and peroxisomes are both endoplasmic reticulum (ER)-derived organelles that fulfill complementary functions in lipid metabolism: Upon nutrient supply, LDs store metabolic energy in the form of neutral lipids and, when energy is needed, supply fatty acids for oxidation in peroxisomes and mitochondria. How these organelles communicate with each other for a concerted metabolic output remains a central question. Here, we summarize recent insights into the biogenesis and function of LDs and peroxisomes with emphasis on the role of PEX19 in these processes.

An alternative membrane topology permits lipid droplet localization of peroxisomal fatty acyl-CoA reductase 1

Fatty acyl-CoA reductase 1 (Far1) is a ubiquitously expressed peroxisomal membrane protein that generates the fatty alcohols required for the biosynthesis of ether lipids. Lipid droplet localization of exogenously expressed and endogenous human Far1 was observed by fluorescence microscopy under conditions of increased triglyceride synthesis in tissue culture cells. This unexpected finding was supported further by correlative light electron microscopy and subcellular fractionation. Selective permeabilization, protease sensitivity and N-glycosylation tagging suggested that Far1 is able to assume two different membrane topologies, differing in the orientation of the short hydrophilic C-terminus towards the lumen or the cytosol, respectively. Two closely spaced hydrophobic domains are contained within the C-terminal region. When analyzed separately, the second domain was sufficient for the localization of a fluorescent reporter to lipid droplets. Targeting of Far1 to lipid droplets was not impaired in either Pex19 or ASNA1 (also known as TRC40) CRISPR/Cas9 knockout cells. In conclusion, our data suggest that Far1 is a novel member of the rather exclusive group of dual topology membrane proteins. At the same time, Far1 shows lipid metabolism-dependent differential subcellular localizations to peroxisomes and lipid droplets.

Dynamics and functions of lipid droplets

Lipid droplets are storage organelles at the centre of lipid and energy homeostasis. They have a unique architecture consisting of a hydrophobic core of neutral lipids, which is enclosed by a phospholipid monolayer that is decorated by a specific set of proteins. Originating from the endoplasmic reticulum, lipid droplets can associate with most other cellular organelles through membrane contact sites. It is becoming apparent that these contacts between lipid droplets and other organelles are highly dynamic and coupled to the cycles of lipid droplet expansion and shrinkage. Importantly, lipid droplet biogenesis and degradation, as well as their interactions with other organelles, are tightly coupled to cellular metabolism and are critical to buffer the levels of toxic lipid species. Thus, lipid droplets facilitate the coordination and communication between different organelles and act as vital hubs of cellular metabolism.

Functions and Mechanisms of the Human Ribosome-Translocon Complex

The membrane of the endoplasmic reticulum (ER) in human cells harbors the protein translocon, which facilitates membrane insertion and translocation of almost every newly synthesized polypeptide targeted to organelles of the secretory pathway. The translocon comprises the polypeptide-conducting Sec61 channel and several additional proteins, which are associated with the heterotrimeric Sec61 complex. This ensemble of proteins facilitates ER targeting of precursor polypeptides, Sec61 channel opening and closing, and modification of precursor polypeptides in transit through the Sec61 complex. Recently, cryoelectron tomography of translocons in native ER membranes has given unprecedented insights into the architecture and dynamics of the native, ribosome-associated translocon and the Sec61 channel. These structural data are discussed in light of different Sec61 channel activities including ribosome receptor function, membrane insertion or translocation of newly synthesized polypeptides as well as the possible roles of the Sec61 channel as a passive ER calcium leak channel and regulator of ATP/ADP exchange between cytosol and ER.

Peroxisome biogenesis, membrane contact sites, and quality control

Peroxisomes are conserved organelles of eukaryotic cells with important roles in cellular metabolism, human health, redox homeostasis, as well as intracellular metabolite transfer and signaling. We review here the current status of the different co-existing modes of biogenesis of peroxisomal membrane proteins demonstrating the fascinating adaptability in their targeting and sorting pathways. While earlier studies focused on peroxisomes as autonomous organelles, the necessity of the ER and potentially even mitochondria as sources of peroxisomal membrane proteins and lipids has come to light in recent years. Additionally, the intimate physical juxtaposition of peroxisomes with other organelles has transitioned from being viewed as random encounters to a growing appreciation of the expanding roles of such inter-organellar membrane contact sites in metabolic and regulatory functions. Peroxisomal quality control mechanisms have also come of age with a variety of mechanisms operating both during biogenesis and in the cellular response to environmental cues.

Moving out but keeping in touch: contacts between endoplasmic reticulum and lipid droplets

The formation of neutral lipid filled and phospholipid monolayer engulfed lipid droplets (LDs) from the bilayer of the endoplasmic reticulum (ER) is an active area of investigation. This process harnesses the biophysical properties of the lipids involved and necessitates cooperation of protein machineries in both organelle membranes. Increasing evidence suggests that once formed, LDs keep close contact to the mother organelle and that this may be achieved via several, morphologically distinct and potentially functionally specialized connections. These may help LDs to dynamically respond to changes in lipid metabolic status sensed by the ER. In this review, we will discuss recent progress in understanding how LDs interact with the ER.

Proteomic analysis of monolayer-integrated proteins on lipid droplets identifies amphipathic interfacial α-helical membrane anchors

Despite not spanning phospholipid bilayers, monotopic integral proteins (MIPs) play critical roles in organizing biochemical reactions on membrane surfaces. Defining the structural basis by which these proteins are anchored to membranes has been hampered by the paucity of unambiguously identified MIPs and a lack of computational tools that accurately distinguish monolayer-integrating motifs from bilayer-spanning transmembrane domains (TMDs). We used quantitative proteomics and statistical modeling to identify 87 high-confidence candidate MIPs in lipid droplets, including 21 proteins with predicted TMDs that cannot be accommodated in these monolayer-enveloped organelles. Systematic cysteine-scanning mutagenesis showed the predicted TMD of one candidate MIP, DHRS3, to be a partially buried amphipathic α-helix in both lipid droplet monolayers and the cytoplasmic leaflet of endoplasmic reticulum membrane bilayers. Coarse-grained molecular dynamics simulations support these observations, suggesting that this helix is most stable at the solvent-membrane interface. The simulations also predicted similar interfacial amphipathic helices when applied to seven additional MIPs from our dataset. Our findings suggest that interfacial helices may be a common motif by which MIPs are integrated into membranes, and provide high-throughput methods to identify and study MIPs.

Seipin and the membrane-shaping protein Pex30 cooperate in organelle budding from the endoplasmic reticulum

Lipid droplets (LDs) and peroxisomes are ubiquitous organelles with central roles in eukaryotic cells. Although the mechanisms involved in biogenesis of these organelles remain elusive, both seem to require the endoplasmic reticulum (ER). Here we show that in yeast the ER budding of these structurally unrelated organelles has remarkably similar requirements and involves cooperation between Pex30 and the seipin complex. In the absence of these components, budding of both LDs and peroxisomes is inhibited, leading to the ER accumulation of their respective constituent molecules, such as triacylglycerols and peroxisomal membrane proteins, whereas COPII vesicle formation remains unaffected. This phenotype can be reversed by remodeling ER phospholipid composition highlighting a key function of these lipids in organelle biogenesis. We propose that seipin and Pex30 act in concert to organize membrane domains permissive for organelle budding, and that may have a lipid composition distinct from the bulk ER.

Lipid droplet and peroxisome biogenesis occur at the same ER subdomains

Nascent lipid droplet (LD) formation occurs in the endoplasmic reticulum (ER) membrane but it is not known how sites of biogenesis are determined. We previously identified ER domains in S. cerevisiae containing the reticulon homology domain (RHD) protein Pex30 that are regions where preperoxisomal vesicles (PPVs) form. Here, we show that Pex30 domains are also sites where most nascent LDs form. Mature LDs usually remain associated with Pex30 subdomains, and the same Pex30 subdomain can simultaneously associate with a LD and a PPV or peroxisome. We find that in higher eukaryotes multiple C2 domain containing transmembrane protein (MCTP2) is similar to Pex30: it contains an RHD and resides in ER domains where most nascent LD biogenesis occurs and that often associate with peroxisomes. Together, these findings indicate that most LDs and PPVs form and remain associated with conserved ER subdomains, and suggest a link between LD and peroxisome biogenesis.

Lipid droplets (LDs) and peroxisomes are both generated by budding off the endoplasmic reticulum (ER). Here, the authors show that the yeast protein Pex30 marks ER subdomains where both LD and peroxisome biogenesis occurs, and identify MCTP2 as the putative mammalian Pex30 ortholog.

Targeting and translocation of proteins to the endoplasmic reticulum at a glance

The evolutionary emergence of organelles was a defining process in diversifying biochemical reactions within the cell and enabling multicellularity. However, compartmentalization also imposed a great challenge-the need to import proteins synthesized in the cytosol into their respective sites of function. For example, one-third of all genes encode for proteins that must be targeted and translocated into the endoplasmic reticulum (ER), which serves as the entry site to the majority of endomembrane compartments. Decades of research have set down the fundamental principles of how proteins get from the cytosol into the ER, and recent studies have brought forward new pathways and additional regulators enabling better definition of the rules governing substrate recognition. In this Cell Science at a Glance article and the accompanying poster, we give an overview of our current understanding of the multifaceted and regulated processes of protein targeting and translocation to the ER.

ESCRT-III is required for scissioning new peroxisomes from the endoplasmic reticulum

Dynamic control of peroxisome proliferation is integral to the peroxisome's many functions. The endoplasmic reticulum (ER) serves as a source of preperoxisomal vesicles (PPVs) that mature into peroxisomes during de novo peroxisome biogenesis and support growth and division of existing peroxisomes. However, the mechanism of PPV formation and release from the ER remains poorly understood. In this study, we show that endosomal sorting complexes required for transport (ESCRT)-III are required to release PPVs budding from the ER into the cytosol. Absence of ESCRT-III proteins impedes de novo peroxisome formation and results in an aberrant peroxisome population in vivo. Using a cell-free PPV budding assay, we show that ESCRT-III proteins Vps20 and Snf7 are necessary to release PPVs from the ER. ESCRT-III is therefore a positive effector of membrane scission for vesicles budding both away from and toward the cytosol. These findings have important implications for the evolutionary timing of emergence of peroxisomes and the rest of the internal membrane architecture of the eukaryotic cell.

Unloosing the Gordian knot of peroxisome formation

Peroxisome biogenesis is governed by molecular machineries, which are either unique to peroxisomes or are partially shared with mitochondria. As peroxisomes have important protective functions in the cell, modulation of their number is important for human health and disease. Significant progress has been made towards our understanding of the mechanisms of peroxisome formation, revealing a remarkable plasticity of the peroxisome biogenesis pathway. Here we discuss most recent findings with particular focus on peroxisome formation in mammalian cells.

Lipid Droplets as Organelles

Long considered inert fat storage depots, it has become clear that lipid droplets (LDs) are bona fide organelles. Like other organelles, they have a characteristic complement of proteins and lipids, and undergo a life cycle that includes biogenesis, maturation, interactions with other organelles, and turnover. I will discuss recent insights into mechanisms governing the life cycle of LDs, and compare and contrast the LD life cycle with that of other metabolic organelles such as mitochondria, peroxisomes, and autophagosomes, highlighting open questions in the field.

The peroxisome biogenesis factors posttranslationally target reticulon homology domain-containing proteins to the endoplasmic reticulum membrane

The endoplasmic reticulum (ER) is shaped by a class of membrane proteins containing reticulon homology domain (RHD), the conserved hydrophobic domain encompassing two short hairpin transmembrane domains. RHD resides in the outer leaflet of the ER membrane, generating high-curvature ER membrane. While most of the membrane proteins destined to enter the secretory pathway are cotranslationally targeted and inserted into ER membrane, the molecular mechanism how the RHD-containing proteins are targeted and inserted into the ER membrane remains to be clarified. Here we show that RHD-containing proteins can be posttranslationally targeted to the ER membrane. PEX19, a cytosolic peroxin, selectively recognizes the nascent RHD-containing proteins and mediates their posttranslational targeting in cooperation with PEX3, a membrane peroxin. Thus, these peroxisome biogenesis factors provide an alternative posttranslational route for membrane insertion of the RHD-containing proteins, implying that ER membrane shaping and peroxisome biogenesis may be coordinated by the posttranslational membrane insertion.

Peroxisome Function, Biogenesis, and Dynamics in Plants

Recent advances highlight understanding of the diversity of peroxisome contributions to plant biology and the mechanisms through which these essential organelles are generated.

Haploid Mammalian Genetic Screen Identifies UBXD8 as a Key Determinant of HMGCR Degradation and Cholesterol Biosynthesis

Supplemental Digital Content is available in the text.

Objective—

The cellular demand for cholesterol requires control of its biosynthesis by the mevalonate pathway. Regulation of HMGCR (3-hydroxy-3-methylglutaryl coenzyme A reductase), a rate-limiting enzyme in this pathway and the target of statins, is a key control point herein. Accordingly, HMGCR is subject to negative and positive regulation. In particular, the ability of oxysterols and intermediates of the mevalonate pathway to stimulate its proteasomal degradation is an exquisite example of metabolically controlled feedback regulation. To define the genetic determinants that govern this process, we conducted an unbiased haploid mammalian genetic screen.

Approach and Results—

We generated human haploid cells with mNeon fused to endogenous HMGCR using CRISPR/Cas9 and used these cells to interrogate regulation of HMGCR abundance in live cells. This resulted in identification of known and new regulators of HMGCR, and among the latter, UBXD8 (ubiquitin regulatory X domain-containing protein 8), a gene that has not been previously implicated in this process. We demonstrate that UBXD8 is an essential determinant of metabolically stimulated degradation of HMGCR and of cholesterol biosynthesis in multiple cell types. Accordingly, UBXD8 ablation leads to aberrant cholesterol synthesis due to loss of feedback control. Mechanistically, we show that UBXD8 is necessary for sterol-stimulated dislocation of ubiquitylated HMGCR from the endoplasmic reticulum membrane en route to proteasomal degradation, a function dependent on its UBX domain.

Conclusions—

We establish UBXD8 as a previously unrecognized determinant that couples flux across the mevalonate pathway to control of cholesterol synthesis and demonstrate the feasibility of applying mammalian haploid genetics to study metabolic traits.

New insights into the distribution, protein abundance and subcellular localisation of the endogenous peroxisomal biogenesis proteins PEX3 and PEX19 in different organs and cell types of the adult mouse

Peroxisomes are ubiquitous organelles mainly involved in ROS and lipid metabolism. Their abundance, protein composition and metabolic function vary depending on the cell type and adjust to different intracellular and environmental factors such as oxidative stress or nutrition. The biogenesis and proliferation of these important organelles are regulated by proteins belonging to the peroxin (PEX) family. PEX3, an integral peroxisomal membrane protein, and the cytosolic shuttling receptor PEX19 are thought to be responsible for the early steps of peroxisome biogenesis and assembly of their matrix protein import machinery. Recently, both peroxins were suggested to be also involved in the autophagy of peroxisomes (pexophagy). Despite the fact that distribution and intracellular abundance of these proteins might regulate the turnover of the peroxisomal compartment in a cell type-specific manner, a comprehensive analysis of the endogenous PEX3 and PEX19 distribution in different organs is still missing. In this study, we have therefore generated antibodies against endogenous mouse PEX3 and PEX19 and analysed their abundance and subcellular localisation in various mouse organs, tissues and cell types and compared it to the one of three commonly used peroxisomal markers (PEX14, ABCD3 and catalase). Our results revealed that the abundance of PEX3, PEX19, PEX14, ABCD3 and catalase strongly varies in the analysed organs and cell types, suggesting that peroxisome abundance, biogenesis and matrix protein import are independently regulated. We further found that in some organs, such as heart and skeletal muscle, the majority of the shuttling receptor PEX19 is bound to the peroxisomal membrane and that a strong variability exists in the cell type-specific ratio of cytosol- and peroxisome-associated PEX19. In conclusion, our results indicate that peroxisomes in various cell types are heterogeneous with regards to their matrix, membrane and biogenesis proteins.

Lipid Droplet Biogenesis

Lipid droplets (LDs) are ubiquitous organelles that store neutral lipids for energy or membrane synthesis and act as hubs for metabolic processes. Cells generate LDs de novo, converting cells to emulsions with LDs constituting the dispersed oil phase in the aqueous cytoplasm. Here we review our current view of LD biogenesis. We present a model of LD formation from the ER in distinct steps and highlight the biology of proteins that govern this biophysical process. Areas of incomplete knowledge are identified, as are connections with physiology and diseases linked to alterations in LD biology.

A different kind of love - lipid droplet contact sites

Lipid droplets (LDs) store lipids and hence serve as energy reservoir and as a source for building-blocks for the organelle membrane systems. LD biology therefore depends on tight communication with other organelles. The unique architecture of LDs, consisting of a neutral lipid core shielded by a phospholipid-monolayer, is however an obstacle to bulk-exchange of bilayer-bounded vesicles with other organelles. In recent years, it is emerging that contact sites, places where two organelles are positioned in close proximity allowing vesicle-independent communication, are an important way to integrate LDs into the organellar landscape. However, few LD contact sites have been studied in depth and our understanding of their structure, extent and function is only starting to emerge. Here, we highlight recent findings on the functions of LD contact sites and on the proteins involved in their formation and hypothesize about the unique characteristics of the contact sites formed by these intriguing organelles. This article is part of a Special Issue entitled: Recent Advances in Lipid Droplet Biology edited by Rosalind Coleman and Matthijs Hesselink.

Establishing the lipid droplet proteome: Mechanisms of lipid droplet protein targeting and degradation

Lipid droplets (LDs) are ubiquitous, endoplasmic reticulum (ER)-derived organelles that mediate the sequestration of neutral lipids (e.g. triacylglycerol and sterol esters), providing a dynamic cellular storage depot for rapid lipid mobilization in response to increased cellular demands. LDs have a unique ultrastructure, consisting of a core of neutral lipids encircled by a phospholipid monolayer that is decorated with integral and peripheral proteins. The LD proteome contains numerous lipid metabolic enzymes, regulatory scaffold proteins, proteins involved in LD clustering and fusion, and other proteins of unknown functions. The cellular role of LDs is inherently determined by the composition of its proteome and alteration of the LD protein coat provides a powerful mechanism to adapt LDs to fluctuating metabolic states. Here, we review the current understanding of the molecular mechanisms that govern LD protein targeting and degradation. This article is part of a Special Issue entitled: Recent Advances in Lipid Droplet Biology edited by Rosalind Coleman and Matthijs Hesselink.