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Abstract

Ceramides, as key components of cellular membranes, play essential roles in various cellular processes, including apoptosis, cell proliferation, and cell signaling. Ceramides are the precursors of all complex sphingolipids in eukaryotic cells. They are synthesized in the endoplasmic reticulum and are further processed at the Golgi apparatus. Therefore, ceramides have to be transported between these two organelles. In mammalian cells, the ceramide transfer protein forms a contact site between the ER and the trans-Golgi region and transports ceramide utilizing its steroidogenic acute regulatory protein-related lipid transfer domain. In yeast, multiple mechanisms of nonvesicular ceramide transport have been described. This involves the nuclear–vacuolar junction protein Nvj2, the yeast tricalbin proteins, and the lipocalin-like protein Svf1. This review aims to provide a comprehensive overview of nonvesicular ceramide transport mechanisms and their relevance in cellular physiology. We will highlight the physiological and pathological consequences of perturbations in nonvesicular ceramide transport and discuss future challenges in identifying and analyzing ceramide transfer proteins.

Keywords

ceramide transport ceramide transport protein Nvj2 Svf1 tricalbins

Introduction

Ceramide, an essential lipid molecule, serves as the fundamental building block for complex sphingolipids and plays a pivotal role in cellular signaling pathways and the regulation of cell death. Dysregulated levels of ceramide have been implicated in the pathogenesis of various neurodegenerative disorders, diabetes, and cardiovascular diseases (Boon et al., 2013; Mielke et al., 2013; Hilvo et al., 2020). Therefore, gaining a comprehensive understanding of ceramide metabolism and its transport between organelles is very important. Here, we will review the current knowledge surrounding ceramide transfer proteins.

Ceramide is synthesized at the endoplasmic reticulum (ER). The first and rate-limiting step in sphingolipid biosynthesis is the condensation of serine and palmitoyl coenzyme A at the cytosolic leaflet of the ER membrane by the serine palmitoyl transferase (SPT) (Hanada, 2003; Lowther et al., 2012). The resulting product, three keto-sphinganine is rapidly reduced to dihydrosphingosine (DHS) by the three keto-dihydrosphingosine reductase (Figure 1). The ceramide synthase (CerS) amide links DHS with a fatty acid to produce ceramide, the backbone of all complex SPs (Hannun and Obeid, 2018). This reaction occurs in the ER membrane. In yeast, the CerS consists of two catalytic subunits Lac1 and Lag1, and one accessory subunit Lip1 (Guillas et al., 2001; Schorling et al., 2001; Vallee and Riezman, 2005). While Lac1 and Lag1 are nonessential and able to compensate for the loss of each other, Lip1 is essential for CerS activity, but its function is unknown (Jiang et al., 1998; Barz and Walter, 1999; Schorling et al., 2001). In mammals, ceramide is synthesized by six different ceramide synthases (CerS1-6). Each enzyme prefers a defined length of fatty acyl-CoA, for example, CerS2 incorporates mainly C22-24-CoAs into ceramides while CerS4 prefers C18-C20-CoA (Laviad et al., 2008; Tidhar et al., 2012, 2018). In yeast, mainly VLCFA-CoA with a length of 26 carbon atoms is used. In the Golgi apparatus, headgroups are attached to ceramide, yielding complex SPs and glycosphingolipids. Consequently, ceramide needs to be transported from the ER to the Golgi. In both, mammalian and yeast cells the rate-limiting SPT is regulated by ER ceramide levels further highlighting the importance of its transport out of the ER (Davis et al., 2019; Schäfer et al., 2023; Xie et al., 2023). In yeast, it has been described that up to 80% of the ceramides are transported to the cis-Golgi via coat protein complex II (COPII)-coated vesicles (Funato and Riezman, 2001; Sato and Nakano, 2007; Miller and Barlowe, 2010). In mammalian cells, only VLCFA-containing ceramides are hypothesized to be transported by vesicular transport to the Golgi apparatus. However, in this review, we will focus on the known mechanisms of nonvesicular ceramide transport.

Figure 1.

Overview of sphingolipid metabolism. A schematic representation of the sphingolipid metabolism in yeast and mammals is depicted. The metabolic pathways are outlined, highlighting the sequential steps through which sphingolipids are synthesized and metabolized within the cell. Key enzymes and their corresponding genes responsible for catalyzing the different reactions are depicted, along with the intermediate molecules formed at each stage. The sspatial distribution of these enzymatic reactions within the cellular compartments is illustrated, emphasizing the significance of inter organelle transport of ceramide. For simplicity, only sphingomyelin and glucosyl-ceramide are shown as complex sphingolipids in mammalian cells.

Nonvesicular Transport of Lipids

Proteins synthesized in the ER are primarily transported via vesicles to the cis-Golgi for sorting and further directed to specific organelles. Consequently, lipids necessary to form membrane vesicles also utilize the same transport machinery. However, to maintain lipid homeostasis and organelle-specific composition, lipids are also transported individually by lipid transfer proteins (LTPs) (Wong et al., 2019). These proteins operate at membrane contact sites (MCSs) where two membranes are in close proximity, up to 30 nm apart (Helle et al., 2013). LTPs reside at various MCSs, such as between the ER and plasma membrane (PM), ER and endosome, ER and vacuole/lysosome, and ER and Golgi (Eisenberg-Bord et al., 2016). This nonvesicular transport occurs either within the concentration gradient of specific lipids or against it, requiring energy. One well-described LTP is the oxysterol-binding protein (OSBP) (Mesmin et al., 2013). OSBP transports sterols from the ER to the trans-Golgi where it is exchanged for phosphatidylinositol-4-phosphate which is subsequently transported to the ER. In the ER, PI4P is hydrolyzed to PI by the PI4P-phosphatase Sac1 (Beh et al., 2001; Levine and Munro, 2001; Raychaudhuri and Prinz, 2010; Stefan et al., 2011; Zewe et al., 2018).

Ceramide Transfer Proteins in Mammalian Cells

The ceramide transport protein (CERT) plays a critical role in the intracellular transportation of ceramides from the ER to the Golgi in mammals. This cytosolic protein, with a size of 68 kDa, functions by collecting newly synthesized ceramides at the ER and facilitating their transfer to the trans-Golgi (Hanada et al., 2003; Kawano et al., 2006; Mizuike et al., 2023). CERT encompasses various functional domains and motifs, similar to other lipid transfer proteins (LTPs). The C-terminal domain, known as the steroidogenic acute regulatory protein-related lipid transfer (START) domain, is essential for ceramide binding. Within the CERT START domain lies a long amphiphilic cavity ideally suited to pick up one ceramide from donor membranes and release it to acceptor membranes, with specific amino acids at the cavity's tip interacting with the ceramide's amide and hydroxyl groups (Kudo et al., 2008). This hydrophobic cavity is believed to function as a molecular measuring device, akin to the bacterial membrane acyltransferase, PagP (Ahn et al., 2004). Interestingly, CERT exhibits a higher affinity for ceramides containing 14–20 carbon atoms compared to those with longer acyl chains (C22–C24) (Kumagai et al., 2005).

The N-terminus of CERT comprises a Pleckstrin Homology (PH) domain, which specifically binds to phosphatidylinositol 4-monophosphate (PI(4)P) primarily found in the trans-Golgi, thus anchoring the protein to the trans-Golgi (De Matteis et al., 2005). Another important motif is the “two phenylalanines in an acidic tract” (FFAT) motif, which interacts with ER resident VAP family proteins, establishing a bridge-like connection between the ER and Golgi (Kawano et al., 2006). CERT's activity is governed by the serine-repeat motif (SRM), located close to the PH domain. Dephosphorylation of this motif renders CERT active, enabling the transport of ceramides from the ER to the trans-Golgi, while phosphorylation results in inactivity and no ceramide transport. Casein kinase 1 plays a key role in regulating CERT activity, responsible for its inactivation (Kumagai and Hanada, 2019).

Mutations in CERT are linked to the development of intellectual disability syndrome. The SRM motif is a frequent site for mutations that render the protein unresponsive to inactivation by phosphorylation (Murakami et al., 2020; Tamura et al., 2021). Another recent study has identified an additional domain as a hot spot for the occurrence of mutations. This domain was described as the central core domain (CCD). The CCD harbors two coiled-coil structures and may function as a dimer interface for dimeric CERT arrangement (Gehin et al., 2023). Other studies have described a trimeric arrangement of CERT (Revert et al., 2018; Goto et al., 2022). How the protein switches between monomeric, dimeric, and trimeric states, and which ones affect CERT function, remains to be revealed in the future. However, all identified mutations so far result in higher CERT activity, causing an increased ceramide flux to the trans-Golgi and correlating with lower ceramide concentration in the ER membrane. This most likely reduces SPT inhibition, leading to a concomitant increase in de novo sphingolipid synthesis. It also impairs glycosphingolipid production at the Golgi and the production of dihydrosphingolipids, which can contribute to neuropathology.

Ceramide Transfer Proteins in Yeast Cells

The majority of ceramides in mammalian cells are transported by CERT. As previously mentioned, ceramides in yeast cells are transported through both vesicular and non-vesicular mechanisms. Concerning the nonvesicular ceramide transport pathways in yeast, Nvj2-dependent ceramide transport, tricalbin-dependent ceramide transport, and Svf1-dependent ceramide transport have been described.

Nvj2 is a component of the nuclear vacuolar junction, an MCS between the nuclear ER and the vacuole in yeast cells. It possesses one transmembrane domain embedded in the ER membrane, with the remaining part of the protein protruding into the cytosol. Notably, Nvj2 shares a common structural feature with the CERT protein—the PH domain, which also binds to PI4P. Additionally, Nvj2 contains a synaptotagmin-like mitochondrial lipid-binding protein (SMP) domain that potentially facilitates ceramide transport (Toulmay and Prinz, 2012; Liu et al., 2017). Furthermore, other studies describe SMP domains as lipid transfer domains (Schauder et al., 2014; AhYoung et al., 2015; Yu et al., 2016).

Recent findings have demonstrated that under ER stress conditions, Nvj2 localizes to the ER-Golgi MCSs and the medial-Golgi, thereby promoting tethering of the MCS and supporting ceramide transport from the ER to the medial-Golgi (Liu et al., 2017). The authors show both, a reduction in complex sphingolipids with a concomitant increase in ceramides. In addition, mutations in the SMP abolish these phenotypes, supporting the direct role of Nvj2 in ceramide transport. However, under nonstress conditions, Njv2 does not localize within the ER-Golgi MCS, yet ceramide transport to the Golgi still occurs when the secretory pathway is blocked in nvj2Δ cells. These observations suggest that other pathways may be involved in ceramide transport (Kopec et al., 2010; Toulmay and Prinz, 2012; Liu et al., 2017).

One potential pathway is mediated by the tricalbin proteins that have been described as potential ceramide transfer proteins between the ER and the medial Golgi (Ikeda et al., 2020). The tricalbins (Tcb1, Tcb2, and Tcb3) share homology with the extended synaptotagmins (E-Syts) that play a role in the formation of MCSs (Giordano et al., 2013; Yu et al., 2016; Bian et al., 2018). Tricalbins possess a hydrophobic N-terminus forming a hairpin motif that anchors to the ER membrane (Hoffmann et al., 2019). This domain senses membrane curvature and prefers membranes with high curvature. To establish a bridge-like connection between two organelles the protein contains also multiple C2 domains that bind membranes in the presence of cytosolic Ca²⁺ (Schulz and Creutz, 2004; Hoffmann et al., 2019). Additionally, they also feature an SMP domain, suggesting a potential role in lipid transfer (Alva and Lupas, 2016; Wong and Levine, 2017). Various studies have associated these proteins with tethering functions at MCSs, either between the cER and PM or between the ER and medial-Golgi (Manford et al., 2012; Toulmay and Prinz, 2012; Collado et al., 2019; Hoffmann et al., 2019; Ikeda et al., 2020; Qian et al., 2021). The latter is proposed to occur during ER stress and promotes nonvesicular ceramide transport from the ER to the Golgi for complex SP synthesis. In tcb1Δ, tcb2Δ, and tcb3Δ cells, the ER–Golgi contact is reduced and acyl ceramide levels are increased. Acylceramide can be stored in lipid droplets (LDs) (Voynova et al., 2012). Its accumulation seems to stimulate LD formation (Ikeda et al., 2020).

Whether Nvj2 or the tricalbins directly transport ceramide with their SMP domains or promoting the MCS establishment, thus supporting indirect nonvesicular ceramide transport from the ER to the Golgi is still unclear and further investigation is required to elucidate their specific role. Whether the mammalian Nvj2 homolog Tex2 transports ceramides is currently unknown.

Finally, survival factor one (Svf1) was recently described as a potential ceramide transfer protein acting at the interface of the ER and the cis-Golgi (Limar et al., 2023). Svf1 is classified as a lipocalin protein. This protein family is known for its transport of small hydrophobic molecules such as steroids, fatty acids, retinoids, prostaglandins, and hormones (Flower, 1994; Chu et al., 1998). They are small circulatory proteins and their typically shape is given by an eight to ten-stranded antiparallel ß-sheet forming a ß-barrel closing itself via hydrogen bonds. Thereby it is flattened or elliptical in cross-sections. The internal ligand binding site is embedded in the tunnel-like structure and covered by a lid which is typically localized between the first two N-terminal ß-sheets. The lid can be either completely closed or partially opened (Flower et al., 1993; Flower, 1996). The family shows a low sequence homology, often below 20%, which makes the identification of clear homologs almost impossible. However, three large structurally conserved regions (SCRs) are found in nearly all proteins of the lipocalin family. The SCR1 includes the first strand and a 3₁₀-like helix, the SCR2 localized within strands six and seven linked by a conserved loop and the SCR3 refers to strand eight and adjoining residues (Flower et al., 1991, 1993). One member of the lipocalin family, the tear lipocalin has been shown to directly interact with ceramide (Glasgow and Abduragimov, 2018).

Interestingly, Svf1 possesses two lipocalin domains, creating a hydrophobic cleft that enables it to accommodate ceramides based on molecular docking studies and targeted lipidomics. When SVF1 is deleted, ceramides accumulate, and complex sphingolipids (SPs) decrease, suggesting that Svf1 acts as a transporter, shuttling ceramides between the endoplasmic reticulum and the Golgi apparatus. Svf1 localizes dynamically to the cis-Golgi apparatus and a cytosolic pool, and immune-purification of Svf1 reveals potential interaction partners from both the ER and Golgi organelles. For Golgi targeting, Svf1 relies on its N-terminal-AH helix and N-terminal acetylation, similar to other proteins targeting the Golgi via an AH (Behnia et al., 2007; Limar et al., 2023). Whether Svf1 acts as a monomer or in a multimeric form remains unknown. The proposed model suggests that Svf1 picks up ceramides from the ER, transiently interacts with it, and then targets the Golgi via its AH, releasing the ceramides for complex SP biosynthesis (Figure 2). The mechanism of ceramide release from the hydrophobic pocket of Svf1 remains uncertain, but one possible model involves exchange with another lipid at the Golgi apparatus, such as diacylglycerol (DAG), a product of complex SP biosynthesis. This is similar to CERT which has been shown to transport DAGs with lower affinity than ceramides (Kumagai et al., 2005). However, since ceramides are rapidly converted into complex SPs the abundance of DAG at the Golgi membrane could be sufficient.

Figure 2.

Model for the various ceramide transport pathways between the ER and the Golgi apparatus. The model depicts the CERT-mediated ceramide transfer in mammalian cells (left side) as well as some potential ceramide transport in COP-II vesicles. In yeast cells (right side), the potential mechanisms for Svf1-mediated ceramide transfer, tricalbin-mediated ceramide transfer, and the stress-induced Nvj2-dependent ceramide transfer between the ER and the Golgi are shown. Ceramides in yeast cells are also transported via COP-II-mediated transport. ER = endoplasmic reticulum; CERT = ceramide transport protein; COP-II = cis-Golgi via coat protein complex II.

Future Directions and Concluding Remarks

For CERT, in vitro assays directly showing ceramide transfer have been established using liposome-based transfer assays (Hanada et al., 2003). Additionally, structural analysis revealed the direct binding of CERT to ceramide (Figure 3a) (Kudo et al., 2008). Furthermore, a photoactivatable and clickable ceramide (paCer) has been used to identify STARD7, along with CERT, as a ceramide-binding homolog, even though it lacks the transport activity of CERT (Bockelmann et al., 2018). Bi-functional and tri-functional ceramides and lipids are becoming more available and will allow the identification and study of ceramide transfer proteins in the future (Kol et al., 2019; Morstein et al., 2021). Importantly, ceramides harboring very long-chain fatty acids make in vitro studies, such as ceramide transfer assays and structural biology approaches, more challenging. VLCFA-containing ceramides are highly hydrophobic and difficult to solubilize. Thus, generating C26 ceramide-containing liposomes for direct ceramide transfer assays remains challenging. Consequently, it still remains unclear if VLCFA-containing ceramides in mammals are transported by a vesicular or nonvesicular pathway. In yeast, all ceramides and complex sphingolipids harbor VLCFAs. This might be one reason why most studies have used the levels of ceramides and complex sphingolipids as a readout for ceramide transfer (Liu et al., 2017; Ikeda et al., 2020; Limar et al., 2023). However, the levels of complex sphingolipids in yeast are also challenging to analyze by mass spectrometry-based lipidomics since no adequate standards for their quantification are commercially available. A major step forward in the analysis of ceramide transfer and binding proteins is also the structure prediction tools using AlphaFold (Jumper et al., 2021; Varadi et al., 2022). In combination with molecular dynamics simulations, this allows predictions of the binding mode of ceramides to proteins (Figure 3b). However, these predictions still require experimental validation using biochemical methods.

Figure 3.

Analysis of the interaction of proteins and ceramides. (a) Crystal structure of the START domain of ceramide bound to C6: ceramide as a ligand (modified from PDB: 2E3N) (Kudo et al., 2008) shows the interaction of a hydrophobic pocket with the C6 cceramide (gray). (b) Molecular docking studies with C26 ceramide and the yeast protein Svf1 (Limar et al., 2023). A typical yeast 44:0;4 ceramide (purple) is modeled into the hydrophobic pocket between the two lipocalin domains of yeast Svf1. The AlphaFold prediction of Svf1 (AF-Q05515-F1) was used for the docking studies. ©2023 Limar et al. Originally published in Journal of Cell Biology https://doi.org/10.1083/jcb.202109162

Footnotes

Declaration of Conflicting Interests

The authors declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.

Funding

The authors disclosed receipt of the following financial support for the research, authorship, and/or publication of this article: This work was supported by the Deutsche Forschungsgemeinschaft, (grant number FR 3647/3-1, FR3647/4-1, SFB 1557 P6).

ORCID iD

Florian Fröhlich

References

Ahn

Engel

Chen

Hwang

Kay

Bishop

Prive

(2004). A hydrocarbon ruler measures palmitate in the enzymatic acylation of endotoxin. EMBO J 23, 2931–2941. doi: 10.1038/sj.emboj.7600320

AhYoung

Jiang

Zhang

Khoi Dang

Loo

Zhou

Egea

(2015). Conserved SMP domains of the ERMES complex bind phospholipids and mediate tether assembly. Proc Natl Acad Sci U S A 112, E3179–E3188. doi: 10.1073/pnas.1422363112

Alva

Lupas

(2016). The TULIP superfamily of eukaryotic lipid-binding proteins as a mediator of lipid sensing and transport. Biochim Biophys Acta 1861, 913–923. doi: 10.1016/j.bbalip.2016.01.016

Barz

Walter

(1999). Two endoplasmic reticulum (ER) membrane proteins that facilitate ER-to-Golgi transport of glycosylphosphatidylinositol-anchored proteins. Mol Biol Cell 10, 1043–1059. doi: 10.1091/mbc.10.4.1043

Beh

Cool

Phillips

Rine

(2001). Overlapping functions of the yeast oxysterol-binding protein homologs. Genetics 157, 1117–1140. doi: 10.1093/genetics/157.3.1117

Behnia

Barr

Flanagan

Barlowe

Munro

(2007). The yeast orthologue of GRASP65 forms a complex with a coiled-coil protein that contributes to ER to Golgi traffic. J Cell Biol 176, 255–261. doi: 10.1083/jcb.200607151

Bian

Saheki

De Camilli

(2018). Ca(2+) releases E-Syt1 autoinhibition to couple ER–plasma membrane tethering with lipid transport. EMBO J 37, 219–234. doi: 10.15252/embj.201797359

Bockelmann

Mina

JGM

Korneev

Hassan

Muller

Hilderink

Vlieg

Raijmakers

Heck

AJR

Haberkant

Holthuis

JCM

, et al. (2018). A search for ceramide binding proteins using bifunctional lipid analogs yields CERT-related protein StarD7. J Lipid Res 59, 515–530. doi: 10.1194/jlr.M082354

Boon

Hoy

Stark

Brown

Meex

Henstridge

Schenk

Meikle

Horowitz

Kingwell

, et al. (2013). Ceramides contained in LDL are elevated in type 2 diabetes and promote inflammation and skeletal muscle insulin resistance. Diabetes 62, 401–410. doi: 10.2337/db12-0686

10.

Chu

Lin

Huang

Chen

(1998). The hydrophobic pocket of 24p3 protein from mouse uterine luminal fluid: fatty acid and retinol binding activity and predicted structural similarity to lipocalins. J Pept Res 52, 390–397. doi: 10.1111/j.1399-3011.1998.tb00663.x

11.

Collado

Kalemanov

Campelo

Bourgoint

Thomas

Loewith

Martinez-Sanchez

Baumeister

Stefan

Fernandez-Busnadiego

, et al. (2019). Tricalbin-mediated contact sites control ER curvature to maintain plasma membrane integrity. Dev Cell 51, 476–487 e477. doi: 10.1016/j.devcel.2019.10.018

12.

Davis

Gable

Suemitsu

Dunn

Wattenberg

(2019). The ORMDL/Orm-serine palmitoyltransferase (SPT) complex is directly regulated by ceramide: reconstitution of SPT regulation in isolated membranes. J Biol Chem 294, 5146–5156. doi: 10.1074/jbc.RA118.007291

13.

De Matteis

Di Campli

Godi

(2005). The role of the phosphoinositides at the Golgi complex. Biochim Biophys Acta 1744, 396–405. doi: 10.1016/j.bbamcr.2005.04.013

14.

Eisenberg-Bord

Shai

Schuldiner

Bohnert

(2016). A tether is a tether is a tether: tethering at membrane contact sites. Dev Cell 39, 395–409. doi: 10.1016/j.devcel.2016.10.022

15.

Flower

(1994). The lipocalin protein family: a role in cell regulation. FEBS Lett 354, 7–11. doi: 10.1016/0014-5793(94)01078-1

16.

Flower

(1996). The lipocalin protein family: structure and function. Biochem J 318(Pt 1), 1–14. doi: 10.1042/bj3180001

17.

Flower

North

Attwood

(1991). Mouse oncogene protein 24p3 is a member of the lipocalin protein family. Biochem Biophys Res Commun 180, 69–74. doi: 10.1016/s0006-291x(05)81256-2

18.

Flower

North

Attwood

(1993). Structure and sequence relationships in the lipocalins and related proteins. Protein Sci 2, 753–761. doi: 10.1002/pro.5560020507

19.

Funato

Riezman

(2001). Vesicular and nonvesicular transport of ceramide from ER to the Golgi apparatus in yeast. J Cell Biol 155, 949–959. doi: 10.1083/jcb.200105033

20.

Gehin

Lone

Lee

Capolupo

Adeyemi

Gerkes

Stegmann

Lopez-Martin

Bermejo-Sanchez

, et al. (2023). CERT1 mutations perturb human development by disrupting sphingolipid homeostasis. J Clin Invest 133. doi: 10.1172/JCI165019

21.

Giordano

Saheki

Idevall-Hagren

Colombo

Pirruccello

Milosevic

Gracheva

Bagriantsev

Borgese

De Camilli

, et al. (2013). PI(4,5)P(2)-dependent and Ca(2+)-regulated ER–PM interactions mediated by the extended synaptotagmins. Cell 153, 1494–1509. doi: 10.1016/j.cell.2013.05.026

22.

Glasgow

Abduragimov

(2018). Interaction of ceramides and tear lipocalin. Biochim Biophys Acta Mol Cell Biol Lipids 1863, 399–408. doi: 10.1016/j.bbalip.2018.01.004

23.

Goto

Egawa

Tomishige

Yamaji

Shimasaki

Kumagai

Hanada

(2022). Involvement of a cluster of basic amino acids in phosphorylation-dependent functional repression of the ceramide transport protein CERT. Int J Mol Sci 23. doi: 10.3390/ijms23158576

24.

Guillas

Kirchman

Chuard

Pfefferli

Jiang

Jazwinski

Conzelmann

(2001). C26-CoA-dependent ceramide synthesis of Saccharomyces cerevisiae is operated by Lag1p and Lac1p. EMBO J 20, 2655–2665. doi: 10.1093/emboj/20.11.2655

25.

Hanada

(2003). Serine palmitoyltransferase, a key enzyme of sphingolipid metabolism. Biochim Biophys Acta 1632, 16–30. doi: 10.1016/s1388-1981(03)00059-3

26.

Hanada

Kumagai

Yasuda

Miura

Kawano

Fukasawa

Nishijima

(2003). Molecular machinery for non-vesicular trafficking of ceramide. Nature 426, 803–809. doi: 10.1038/nature02188

27.

Hannun

Obeid

(2018). Sphingolipids and their metabolism in physiology and disease. Nat Rev Mol Cell Biol 19, 175–191. doi: 10.1038/nrm.2017.107

28.

Helle

Kanfer

Kolar

Lang

Michel

Kornmann

(2013). Organization and function of membrane contact sites. Biochim Biophys Acta 1833, 2526–2541. doi: 10.1016/j.bbamcr.2013.01.028

29.

Hilvo

Meikle

Pedersen

Tell

Dhar

Brenner

Schottker

Laaperi

Kauhanen

Koistinen

, et al. (2020). Development and validation of a ceramide- and phospholipid-based cardiovascular risk estimation score for coronary artery disease patients. Eur Heart J 41, 371–380. doi: 10.1093/eurheartj/ehz387

30.

Hoffmann

Bharat

TAM

Wozny

Boulanger

Miller

Kukulski

(2019). Tricalbins contribute to cellular lipid flux and form curved ER–PM contacts that are bridged by rod-shaped structures. Dev Cell 51, 488–502 e488. doi: 10.1016/j.devcel.2019.09.019

31.

Ikeda

Schlarmann

Kurokawa

Nakano

Riezman

Funato

(2020). Tricalbins are required for non-vesicular ceramide transport at ER–Golgi contacts and modulate lipid droplet biogenesis. iScience 23, 101603. doi: 10.1016/j.isci.2020.101603

32.

Jiang

Kirchman

Zagulski

Hunt

Jazwinski

(1998). Homologs of the yeast longevity gene LAG1 in Caenorhabditis elegans and humans. Genome Res 8, 1259–1272. doi: 10.1101/gr.8.12.1259

33.

Jumper

Evans

Pritzel

Green

Figurnov

Ronneberger

Tunyasuvunakool

Bates

Zidek

Potapenko

(2021). Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589. doi: 10.1038/s41586-021-03819-2

34.

Kawano

Kumagai

Nishijima

Hanada

(2006). Efficient trafficking of ceramide from the endoplasmic reticulum to the Golgi apparatus requires a VAMP-associated protein-interacting FFAT motif of CERT. J Biol Chem 281, 30279–30288. doi: 10.1074/jbc.M605032200

35.

Kol

Williams

Toombs-Ruane

Franquelim

Korneev

Schroeer

Schwille

Trauner

Holthuis

Frank

, et al. (2019). Optical manipulation of sphingolipid biosynthesis using photoswitchable ceramides. Elife 8. doi: 10.7554/eLife.43230

36.

Kopec

Alva

Lupas

(2010). Homology of SMP domains to the TULIP superfamily of lipid-binding proteins provides a structural basis for lipid exchange between ER and mitochondria. Bioinformatics 26, 1927–1931. doi: 10.1093/bioinformatics/btq326

37.

Kudo

Kumagai

Tomishige

Yamaji

Wakatsuki

Nishijima

Hanada

Kato

(2008). Structural basis for specific lipid recognition by CERT responsible for nonvesicular trafficking of ceramide. Proc Natl Acad Sci U S A 105, 488–493. doi: 10.1073/pnas.0709191105

38.

Kumagai

Hanada

(2019). Structure, functions and regulation of CERT, a lipid-transfer protein for the delivery of ceramide at the ER–Golgi membrane contact sites. FEBS Lett 593, 2366–2377. doi: 10.1002/1873-3468.13511

39.

Kumagai

Yasuda

Okemoto

Nishijima

Kobayashi

Hanada

(2005). CERT mediates intermembrane transfer of various molecular species of ceramides. J Biol Chem 280, 6488–6495. doi: 10.1074/jbc.M409290200

40.

Laviad

Albee

Pankova-Kholmyansky

Epstein

Park

Merrill

Jr. , Futerman

. (2008). Characterization of ceramide synthase 2: tissue distribution, substrate specificity, and inhibition by sphingosine 1-phosphate. J Biol Chem 283, 5677–5684. doi: 10.1074/jbc.M707386200

41.

Levine

Munro

(2001). Dual targeting of Osh1p, a yeast homologue of oxysterol-binding protein, to both the Golgi and the nucleus–vacuole junction. Mol Biol Cell 12, 1633–1644. doi: 10.1091/mbc.12.6.1633

42.

Limar

Korner

Martinez-Montanes

Stancheva

Wolf

Walter

Miller

Ejsing

Galassi

Frohlich

, et al (2023). Yeast Svf1 binds ceramides and contributes to sphingolipid metabolism at the ER–cis-Golgi interface. J Cell Biol 222. doi: 10.1083/jcb.202109162

43.

Liu

Choudhary

Toulmay

Prinz

(2017). An inducible ER–Golgi tether facilitates ceramide transport to alleviate lipotoxicity. J Cell Biol 216, 131–147. doi: 10.1083/jcb.201606059

44.

Lowther

Naismith

Dunn

Campopiano

(2012). Structural, mechanistic and regulatory studies of serine palmitoyltransferase. Biochem Soc Trans 40, 547–554. doi: 10.1042/BST20110769

45.

Manford

Stefan

Yuan

Macgurn

Emr

(2012). ER-to-plasma membrane tethering proteins regulate cell signaling and ER morphology. Dev Cell 23, 1129–1140. doi: 10.1016/j.devcel.2012.11.004

46.

Mesmin

Bigay

Moser von Filseck

Lacas-Gervais

Drin

Antonny

(2013). A four-step cycle driven by PI(4)P hydrolysis directs sterol/PI(4)P exchange by the ER–Golgi tether OSBP. Cell 155, 830–843. doi: 10.1016/j.cell.2013.09.056

47.

Mielke

Maetzler

Haughey

Bandaru

Savica

Deuschle

Gasser

Hauser

Graber-Sultan

Schleicher

, et al. (2013). Plasma ceramide and glucosylceramide metabolism is altered in sporadic Parkinson’s disease and associated with cognitive impairment: a pilot study. PLoS One 8, e73094. doi: 10.1371/journal.pone.0073094

48.

Miller

Barlowe

(2010). Regulation of coat assembly–sorting things out at the ER. Curr Opin Cell Biol 22, 447–453. doi: 10.1016/j.ceb.2010.04.003

49.

Mizuike

Sakai

Katoh

Yamaji

Hanada

(2023). The C10orf76-PI4KB axis orchestrates CERT-mediated ceramide trafficking to the distal Golgi. J Cell Biol 222. doi: 10.1083/jcb.202111069

50.

Morstein

Kol

Novak

AJE

Feng

Khayyo

Hinnah

Li-Purcell

Pan

Williams

Riezman

, et al. (2021). Short photoswitchable ceramides enable optical control of apoptosis. ACS Chem Biol 16, 452–456. doi: 10.1021/acschembio.0c00823

51.

Murakami

Tamura

Enomoto

Shimasaki

Kurosawa

Hanada

(2020). Intellectual disability-associated gain-of-function mutations in CERT1 that encodes the ceramide transport protein CERT. PLoS One 15, e0243980. doi: 10.1371/journal.pone.0243980

52.

Qian

Wan

Liu

(2021). Calcium-dependent and -independent lipid transfer mediated by tricalbins in yeast. J Biol Chem 296, 100729. doi: 10.1016/j.jbc.2021.100729

53.

Raychaudhuri

Prinz

(2010). The diverse functions of oxysterol-binding proteins. Annu Rev Cell Dev Biol 26, 157–177. doi: 10.1146/annurev.cellbio.042308.113334

54.

Revert

Revert-Ros

Blasco

Artigot

Lopez-Pascual

Gozalbo-Rovira

Ventura

Gutierrez-Carbonell

Roda

Ruiz-Sanchis

, et al. (2018). Selective targeting of collagen IV in the cancer cell microenvironment reduces tumor burden. Oncotarget 9, 11020–11045. doi: 10.18632/oncotarget.24280

55.

Sato

Nakano

(2007). Mechanisms of COPII vesicle formation and protein sorting. FEBS Lett 581, 2076–2082. doi: 10.1016/j.febslet.2007.01.091

56.

Schäfer

J-H

Körner

Esch

Limar

Parey

Walter

Januliene

Moeller

Fröhlich

(2023). Structure of the ceramide-bound SPOTS complex. bioRxiv, 2023.2002.2003.526835. doi: 10.1101/2023.02.03.526835

57.

Schauder

Saheki

Narayanaswamy

Torta

Wenk

De Camilli

Reinisch

(2014). Structure of a lipid-bound extended synaptotagmin indicates a role in lipid transfer. Nature 510, 552–555. doi: 10.1038/nature13269

58.

Schorling

Vallee

Barz

Riezman

Oesterhelt

(2001). Lag1p and Lac1p are essential for the Acyl-CoA-dependent ceramide synthase reaction in Saccharomyces cerevisae. Mol Biol Cell 12, 3417–3427. doi: 10.1091/mbc.12.11.3417

59.

Schulz

Creutz

(2004). The tricalbin C2 domains: lipid-binding properties of a novel, synaptotagmin-like yeast protein family. Biochemistry 43, 3987–3995. doi: 10.1021/bi036082w

60.

Stefan

Manford

Baird

Yamada-Hanff

Mao

Emr

(2011). Osh proteins regulate phosphoinositide metabolism at ER–plasma membrane contact sites. Cell 144, 389–401. doi: 10.1016/j.cell.2010.12.034

61.

Tamura

Sakai

Martorell

Colome

Mizuike

Goto

Ortigoza-Escobar

Hanada

(2021). Intellectual-disability-associated mutations in the ceramide transport protein gene CERT1 lead to aberrant function and subcellular distribution. J Biol Chem 297, 101338. doi: 10.1016/j.jbc.2021.101338

62.

Tidhar

Ben-Dor

Wang

Kelly

Merrill

Futerman

(2012). Acyl chain specificity of ceramide synthases is determined within a region of 150 residues in the Tram-Lag-CLN8 (TLC) domain. J Biol Chem 287, 3197–3206. doi: 10.1074/jbc.M111.280271

63.

Tidhar

Zelnik

Volpert

Ben-Dor

Kelly

Merrill

Futerman

(2018). Eleven residues determine the acyl chain specificity of ceramide synthases. J Biol Chem 293, 9912–9921. doi: 10.1074/jbc.RA118.001936

64.

Toulmay

Prinz

(2012). A conserved membrane-binding domain targets proteins to organelle contact sites. J Cell Sci 125, 49–58. doi: 10.1242/jcs.085118

65.

Vallee

Riezman

(2005). Lip1p: a novel subunit of acyl-CoA ceramide synthase. EMBO J 24, 730–741. doi: 10.1038/sj.emboj.7600562

66.

Varadi

Anyango

Deshpande

Nair

Natassia

Yordanova

Yuan

Stroe

Wood

Laydon

, et al. (2022). Alphafold protein structure database: massively expanding the structural coverage of protein-sequence space with high-accuracy models. Nucleic Acids Res 50, D439–D444. doi: 10.1093/nar/gkab1061

67.

Voynova

Vionnet

Ejsing

Conzelmann

(2012). A novel pathway of ceramide metabolism in Saccharomyces cerevisiae. Biochem J 447, 103–114. doi: 10.1042/BJ20120712

68.

Wong

Gatta

Levine

(2019). Lipid transfer proteins: the lipid commute via shuttles, bridges and tubes. Nat Rev Mol Cell Biol 20, 85–101. doi: 10.1038/s41580-018-0071-5

69.

Wong

Levine

(2017). Tubular lipid binding proteins (TULIPs) growing everywhere. Biochim Biophys Acta Mol Cell Res 1864, 1439–1449. doi: 10.1016/j.bbamcr.2017.05.019

70.

Xie

Liu

Dong

Zhang

Yue

Mahawar

Farooq

Vohra

Fang

, et al. (2023). Ceramide sensing by human SPT-ORMDL complex for establishing sphingolipid homeostasis. Nat Commun 14, 3475. doi: 10.1038/s41467-023-39274-y

71.

Liu

Gulbranson

Paine

Rathore

Shen

(2016). Extended synaptotagmins are Ca2+-dependent lipid transfer proteins at membrane contact sites. Proc Natl Acad Sci U S A 113, 4362–4367. doi: 10.1073/pnas.1517259113

72.

Zewe

Wills

Sangappa

Goulden

Hammond

(2018). SAC1 degrades its lipid substrate PtdIns4P in the endoplasmic reticulum to maintain a steep chemical gradient with donor membranes. Elife 7. doi: 10.7554/eLife.35588

Mechanisms of Nonvesicular Ceramide Transport

Abstract

Keywords

Introduction

Nonvesicular Transport of Lipids

Ceramide Transfer Proteins in Mammalian Cells

Ceramide Transfer Proteins in Yeast Cells

Future Directions and Concluding Remarks

Footnotes

Declaration of Conflicting Interests

Funding

ORCID iD

References