Available online at www.sciencedirect.com

ScienceDirect Modulation of endomembranes morphodynamics in the secretory/retrograde pathways depends on lipid diversity Yohann Boutte´ and Patrick Moreau Membrane lipids are crucial bricks for cell and organelle compartmentalization and their physical properties and interactions with other membrane partners (lipids or proteins) reveal lipids as key actors of the regulation of membrane morphodynamics in many cellular functions and especially in the secretory/retrograde pathways. Studies on membrane models have indicated diverse mechanisms by which membranes bend. Moreover, in vivo studies also indicate that membrane curvature can play crucial roles in the regulation of endomembrane morphodynamics, organelle morphology and transport vesicle formation. A role for enzymes of lipid metabolism and lipid–protein interactions will be discussed as crucial mechanisms in the regulation of membrane morphodynamics in the secretory/retrograde pathways. Addresses Laboratoire de Biogene`se Membranaire, UMR 5200 CNRS, University of Bordeaux, France Corresponding author: Moreau, Patrick ([email protected])

Current Opinion in Plant Biology 2014, 22:22–29 This review comes from a themed issue on Cell biology Edited by Shaul Yalovsky and Viktor Zˇa´rsky´

http://dx.doi.org/10.1016/j.pbi.2014.08.004 1369-5266/# 2014 Elsevier Ltd. All right reserved.

Introduction Membrane lipids have a well known crucial function in cell and organelle compartmentalization. Through interactions of lipids with membrane proteins, lipids play an important function in regulating membrane protein activities. Numerous data demonstrate lipids being involved in signaling processes and being key actors to regulate membrane dynamics in many physiological functions. For example galactolipids, which represent up to 75% of thylakoid lipids, are crucial for thylakoid ultra-structure and photosynthesis efficiency [1]. Cardiolipin, a specific mitochondrial lipid, is essential for mitochondrial morphogenesis, ultra-structure and function [2,3], and its properties make it crucial for mitochondrial fission [3]. Another example is given by the important role of polyphosphoinositides and their Current Opinion in Plant Biology 2014, 22:22–29

corresponding phosphatases in vacuolar functioning and morphology in plant cells [4]. Similarly, eukaryotic secretory/retrograde pathways are also tremendously regulated by the physicochemical properties of membrane lipids [5–8]. In all eukaryotic cells the establishment, maintenance and plasticity of the morphology of organelles is fundamental to their function. Several families of proteins are involved in shaping organelle morphologies [9–11] as exemplified in plants by the reticulons and the atlastin homologue proteins [12,13]. Beside proteins, lipids and enzymes of their metabolism are largely involved in governing the complex mechanisms of membrane dynamics and their regulation in the secretory/retrograde pathways.

Physical properties of lipids impact membrane curvature Studies on membrane models have unraveled many mechanisms by which membranes can bend. Membrane curvature is essential for ER structure and ER exit sites organization and localization at the ER [14,15]. On the protein side, the asymmetric insertion of a protein into a membrane bilayer, the adhesion of a curved protein domain to the membrane surface, the assembly of protein scaffold and membrane protein crowding through protein–protein interactions can be driving forces for membrane curvature and bending [10,11], and the energy cost these forces required has been deeply analyzed [11]. On the lipid side, it has been detailed how diverse lipids can induce membrane curvature [16]. As indicated in Table 1, each lipid can be characterized by a packing parameter (P) where P = v/a.l and v corresponds to the molecular volume, a is related to the cross-sectional area of the head group and l is the length of the molecule [16]. P indicates whether the lipid has the tendency to induce a positive or negative membrane curvature. Most of the roles of specific proteins and lipids in regulating membrane curvature were determined on membrane models and therefore we have to be aware that their implication would have to be also evaluated in membranes where physiological conditions are met [10]. Although it is clear that membrane curvature is playing crucial roles in the regulation of endomembrane morphodynamics, possible discrepancies between in vitro and in vivo systems have definitely not to be underestimated [7]. www.sciencedirect.com

Endomembranes morphodynamics and lipid diversity Boutte´ and Moreau 23

Table 1 Relationship between lipid physical properties, enzymes of lipid metabolism and endomembrane morphodynamics in the secretory/ endocytic pathways of plant cells and other eukaryotic cells. Lipids Lipids: P > 1 (cone-shaped, negative membrane curvature)

Lipids: P < 1 (inverted cone-shaped, positive membrane curvature)

Enzymes and types of actions

Effect on endomembranes

FFA LCB

DAG kinases, PA phosphatases, inhibition of phospholipid metabolism Activation of PLA2 Inhibition of ceramide synthases

PA

Activation of phospholipase D

Sterols

Enzymes of sterol metabolism

lysoPL (LPA, LPC)

Activation of phospholipase A1, PLA2, Inhibition of lysoPL acyltransferases

PIP

PI kinases, Phosphoinositide phosphatases PIP kinases, Phosphoinositide phosphatases

- DAG increase induces Golgi vesiculation. - DAG decrease inhibits Golgi budding. [7,27] Increase of membrane permeability. [20] LCB increase induces ER morphological changes. [36]# - PA increase induces Golgi vesiculation. - PA decrease inhibits Golgi budding. [18,19,22–26]# - Sterol increase induces Golgi vesiculation. - Sterol decrease inhibits Golgi budding. [5,7] - Increase of permeability. - LPC increase induces ER-Golgi tubulation. - Inhibition of LPA acylation disadvantages Golgi budding. [18,19,22–26]# Regulation of membrane budding and trafficking. [49,50,51,52,53]# Regulation of membrane budding and trafficking. [49,50,51,52,53]#

DAG

PIP2

DAG: diacylglycerol; ER: endoplasmic reticulum; FFA: free fatty acids; LCB: Long chain bases; LPA: lysophosphatidic acid; LPC: lysophosphatidylcholine; lysoPL: lysophospholipids; PA: phosphatidic acid; PLA2: phospholipase A2 which hydrolyzes major phospholipids at the sn2 position; PIP: phosphatidylinositol phosphate; PIP2: phosphatidylinositol diphosphate. P (packing parameter) = v/al: v corresponds to the molecular volume, a is related to the cross-sectional area of the head group and l is the length of the lipid molecule [16]. Types of actions on concerned enzymes: either genetic and/or pharmacological approaches were considered. A caution must be highlighted here for all lipids: their effects can be linked either to their biophysical properties, their potential signaling roles or both. # References in italic and bold are concerning plant data.

A role for the Lands cycle and related enzymes in membrane morphodynamics? The Lands cycle involves phospholipases A2 (PLA2) and lysophospholipid acyltransferases (LPAT) to govern fatty acyl remodeling of phospholipids synthesized through the Kennedy pathway [17,18]. PLA2 form lysophospholipids (inverted cone-shaped) that have the propensy to induce local positive membrane curvature (Table 1, Figure 1) and LPAT produce phospholipids with properties that vary depending on the size of their polar head and the unsaturation of their fatty acids. Phospholipids with a small polar head (phosphatidic acid: PA, Table 1; but also phosphatidylethanolamine: PE and phosphatidylserine: PS) can induce negative membrane curvature and favors non-lamellar phases which are known to be involved in membrane fusion/fission processes whereas phosphatidylcholine (PC) which is more cylindrical, either stabilizes the bilayer leaflet or slightly induces a negative membrane curvature when its fatty acids are highly unsaturated. All these activities may therefore regulate the local dynamic state of endomembranes. The pioneering work of Brown and colleagues in animal cells [18] has paved the way to unravel the role of such activities in regulating the dynamics of the Golgi and the emission of Golgi-derived COPI vesicles but also that of ER-derived COPII vesicles [(18, Figure 1)]. The best example in animal cells is the regulation of COPI vesicle versus tubule formation from the Golgi [19]. COPI buds are elongated to form tubules through the activity of cPLA2 which produces lysophosphatidic acid www.sciencedirect.com

(LPA)/lysophosphatidylcholine (LPC) (positive membrane curvature). Contrastingly, LPA acyltransferase and PLD activities which produce PA (negative membrane curvature) govern vesicle formation and fission [19]. The PLA2 is also producing free fatty acid (FFA, negative membrane curvature) which could in theory counteract the effect of LPA/LPC although this is not very likely due to that FFA are diffusing more rapidly than lysophospholipids from one leaflet to the other one [20]. Therefore lysophospholipids are likely to be more concentrated in one of the two leaflets compared to FFA, and that would induce a dynamic asymmetry which helps membrane bending. Such a regulation of vesicles/tubules formation may be a way to control the anterograde and retrograde trafficking within the Golgi complex and towards the ER in animal cells. Very recently, using very high speed and high resolution confocal microscopy, a new model was proposed in yeast where cis-Golgi recovers material from ER export sites via specific contacts [21]. One can easily imagine that specific enzymes of lipid metabolism such as those shown in Figure 1 could be involved in the fusion events associated to the ‘hug-and-kiss’ process proposed between cis-Golgi membranes and the ER export sites in yeast [21]. In plant cells, only very few investigations approached these concepts. Pharmacological and genetic approaches suggested that inhibition of PLA2a impairs PIN protein trafficking in root cells and showed an accumulation of Current Opinion in Plant Biology 2014, 22:22–29

24 Cell biology

Figure 1

PC

de novo glycerolipid synthesis

Lands Cycle

GPAT ∗ LPE Positive curvature

PIP/PIP2 PI-PLC

PC-PLC

PLA 2

LPA ∗ LPC

PE PA

LPAT

DAG

DAGK LPP

Negative curvature

PLD PC

Budding

Fusion / Fission STEP 1 Budding of COPII (ER) and/or COPI (Golgi) vesicles

STEP 2 Fission of COPII (ER) and/or COPI (Golgi) vesicles Current Opinion in Plant Biology

Lands cycle and related enzymes: a link with COP vesicle formation? The Lands cycle involves phospholipases A2 (PLA2) and lysophospholipid acyltransferases (LPAT) which could be a switch for the cell to regulate the formation of transport carriers. PLA2 forms lysophospholipids which induce local positive membrane curvature (Table 1) and LPAT produces phospholipids with different properties (PA, PE and PS induce negative membrane curvature and non-lamellar phases whereas PC and PI either stabilize the bilayer leaflet or slightly induce a negative membrane curvature when highly unsaturated). Beyond the Land cycle, other enzymatic activities regulate the accumulation of different lipid species. All these activities could therefore regulate the local dynamic state of the endomembranes and the formation of transport carriers. A crucial role of the Lands cycle and related enzymes has been demonstrated in animal cells in the case of COP vesicle formation [18,19]. The question is totally open in plant cells to determine whether the Lands cycle and related enzymes have any crucial influence on COP vesicle formation and membranes morphodynamics in general, and this constitutes a challenging area of research in plant cells for the future. The asterisks on GPAT and LPA indicate that GPAT only synthesizes LPA. DAG: diacylglycerol; DAGK: DAG kinase; ER: endoplasmic reticulum; GPAT: glycerol-3-phosphate acyltransferase; LPA: lysophosphatidic acid; LPAT: lysophospholipid acyltransferase; LPC: lysophosphatidylcholine; LPE: lysophosphatidylethanolamine; LPP: lipid phosphate phosphatase; PA: phosphatidic acid; PC: phosphatidylcholine; PC-PLC: phosphatidylcholine phospholipase C; PE: phosphatidylethanolamine; PI-PLC: phosphoinositide phospholipase C; PLA2: phospholipase A2 which hydrolyzes major phospholipids at the sn2 position; PIP: phosphatidylinositol phosphate; PIP2: phosphatidylinositol diphosphate; PLD: phospholipase D.

trans-Golgi network (TGN) vesicles (post-Golgi compartments) in the presence of the inhibitor ONO [22]. In addition, an external application of lysophosphatidylethanolamine (LPE) restored PIN protein transport to the plasma membrane [22]. Similarly, PLA2 b, g and d were shown to have a crucial function in pollen development and tube growth, again with a recovery with LPE [23]. However, it has not yet been determined how (mechanical/biophysical impact, signaling process, among others) Current Opinion in Plant Biology 2014, 22:22–29

PLA2a may affect PIN protein trafficking and the substrates of the various PLA2 have not been determined in vivo. Some phospholipases A may have even wider effects on plant development as illustrated by the effect of the patatin-related phospholipase pPLAIIIb on cellulose content, cell wall production, cell elongation and cell morphology [24], but the real nature of the role(s) of the products of these enzymes have not been clearly established in plant cells. Similarly PLDz2, through the production of PA, was suggested to be involved in the cycling of PIN2-containing vesicles and the regulation of auxin transport [25]. By a multi-inhibitor approach, Pleskot and coworkers [26] have shown that a tight control of the amounts of PA through the regulation of the three enzyme activities PLD, diacylglycerol kinase (DAGK) and lipid-phosphate phosphatase (LPP) (see Figure 1) could be crucial for several aspects of pollen tube growth in Tobacco. Anyway, the question is still open in plant cells whether the Lands cycle and related enzymes (Figure 1) have a crucial influence on membranes morphodynamics as this is strongly suggested in animal cells in the case of COP vesicle formation (Figure 1). This will be an exciting focus for future challenging studies in plant cells.

De novo lipid biosynthesis and lipid translocases are driving forces of membrane morphodynamics In animal and yeast cells, the importance of controlling the amount of a given lipid such as PA, lysophospholipids, DAG or cholesterol can be crucial [5,7,27], for example both an increase and a decrease of cholesterol can block the Golgi secretory function in animal cells [5,7]. In plant cells, it has been shown that a correct membrane sterol composition is crucial for the post-cytokinetic establishment of the polarity of PIN2 [28] and that endocytosis may generally depend on phytosterols in plant cells [28,29]. De novo lipid biosynthesis is expected to be crucial for plant development as illustrated by the cytidine diphosphate diacylglycerol synthase mutants [30] or the myo-inositol-3-phosphate synthase mutants of Arabidopsis thaliana [31]. In some of these mutants, consequences on the morphology of membranes of the secretory/retrograde pathways are observed [31] (endomembranes structure and formation of trafficking vesicles are altered) although no alterations were detectable for some others of these Arabidopsis mutants [30]. A clear link between regulation of membrane morphology and regulation of de novo lipid biosynthesis was given in A. thaliana by the double mutant pah1;pah2 which is knock-down in two genes coding two LPPs (PA phosphohydrolases 1 and 2) [32]. In this pah1;pah2 double mutant, ER expansions are often observed due to deregulation of phospholipid metabolism [32]. Not only phospholipid regulations are crucial for the secretory/retrograde pathways in plants, it was also shown that a decrease of the amount of the www.sciencedirect.com

Endomembranes morphodynamics and lipid diversity Boutte´ and Moreau 25

sphingolipid glucosylceramide partially impaired protein trafficking from the Golgi and disturbed the Golgi structure in plant cells [33]. Moreover, it has been observed that an increase of the amount of proteins to be secreted induced the de novo biosynthesis of glucosylceramide and phytosterols in tobacco leaf epidermal cells [33]. This highlights a relationship between lipid homeostasis and protein transport. Sphingolipid homeostasis is not only involved in cellular processes but has also been linked to various physiological functions [34]. The biosynthesis of very long chain fatty acid-containing sphingolipids was shown to be involved in the polarized transport of auxin [35,36]. Moreover, an increased amount of free long chain bases (LCB) induced a morphological change of the ER network of Arabidopsis [36]. Interestingly, lipid biosynthesis is not the only way for cells to control lipid homeostasis. Lipid transfer proteins and flippases/translocases also contribute to control lipid composition at certain places inside the cell. A glycosphingolipid transfer protein (GLTP1) was discovered in Arabidopsis but whether this protein is acting as other lipid transfer proteins in animal cells such as the CERT or the FAPP2 proteins remains to be clarified [37]. In particular, whether GLTP1 is involved in biosynthesis of sphingolipids or in concentrating sphingolipids to specific membrane domains as FAPP2 in animal cells would be interesting to determine [7,38]. Additionally to lipid transfer proteins, the dynamic process of lipid translocation is also a crucial player in lipid homeostasis at defined spots of membranes. It was determined that variation of less than 1% in the amount of a given lipid between the two leaflets of a membrane bilayer, if concentrated in a specific domain, can have a strong impact on the local membrane structure. The resulting asymmetry can well contribute to membrane curvature and bending. For example, it was determined in vitro with animal cell extracts that the asymmetric distribution of PA and PIP2 in reconstituted vesicles is very crucial for membrane fusion [39]. In addition, phospholipid flippases/ translocases represent a big family of proteins that participate to the formation of transport vesicles from the Golgi and endosomal membranes in animal cells [40]. A recent study in HeLa cells on the asymmetrical structure of the Golgi, as revealed by atomic force microscopy, argues in favor of lipids participating to similar extent as proteins in Golgi morphodynamics in animal cells [41]. In Arabidopsis, mutants of the Golgi P4-ATPase ALA3, involved in lipid translocation, have strong defects in slime vesicle formation [42]. Clearly, a next step is to understand how lipid biosynthesis and translocation can stimulate vesicle budding and fission. Theoretically, positive curvature of the cytosolic leaflet and negative curvature of the luminal leaflet at the bud occurs during vesicle formation from a donor compartment. Rationally, the opposite is found at the neck of www.sciencedirect.com

Figure 2

Lipids segregation

Lipid-protein interaction

Lipid clustering mediates membrane curvature

- Membrane curvature-sensing proteins - Enzymes of lipid metabolism

Vesicle/tubule formation

Vesicle fission Vesicle fission

Lipids for which P 1 : DAG, PA, PE, LCB, Ceramide, Sterols Current Opinion in Plant Biology

Theoretical model summarizing lipid species diversity, lipid metabolism and lipid-protein interactions during formation of vesicle carriers. Lipids with either P values >1 or 1) or inverted cones (P < 1). Lipids with P > 1 tend to favor negative membrane curvature while lipids with P < 1 promote positive membrane curvature. According to the membrane leaflet where lipids reside, positive or negative membrane curvature contributes to either vesicle/ tubule bud formation and/or vesicle fission respectively. Additionally to membrane curvature, vesicle formation and fission are also enhanced by lipid–protein interactions such as those involving membrane curvaturesensing proteins and/or enzymes of lipid metabolism which can be recruited/concentrated to these membrane domains from the cytosol or from the neighboring membrane environment (PLA2 or PI-specific PLC for example). DAG: diacylglycerol; GluCer: glucosylceramide; LCB: long chain base; LysoPL: lysophospholipids; PA: phosphatidic acid; PE: phosphatidylethanolamine; PI: phosphatidylinositol; PIP: phosphatidylinositol phosphate; PIP2: phosphatidylinositol diphosphate.

the vesicle during fission from the donor compartment (Figure 2). Therefore, according to their physical properties (Table 1), lipids with P < 1 are expected to be concentrated in the cytosolic leaflet of the bud and the luminal leaflet at the neck whereas lipids with P > 1 would be expected to be concentrated in the lumenal leaflet of the bud and the cytosolic leaflet at the neck. In this theoretical scheme, locally defined lipid Current Opinion in Plant Biology 2014, 22:22–29

26 Cell biology

metabolism and lipid translocation between leaflets would be driving forces to produce and concentrate crucial lipids in these specific areas of the vesicle.

Membrane domains, lipid–protein interactions and cargo sorting In animal cells, the rapid-partitioning model proposes that phase separation of sphingolipids and glycerophospholipids at the Golgi creates a lipid gradient across cisto-trans cisternae of the Golgi but also within each cisternae [5]. Due to their physical properties, sphingolipids are thought to preferentially associate with non-compact tubular membrane regions and would act in cargo selection [43]. Hence, fluxes of cargoes at the Golgi would depend on distinct membrane structures, for example, tubular versus vesicular [5]. Moreover, sphingolipids and sterols have the ability to auto-associate and to form nanoscale membrane domains referred to as ‘lipid rafts’. In yeast, sphingolipid-enriched and sterol-enriched domains are segregating at post-Golgi compartments (TGN), and are thought to be involved in protein sorting [5,7,8]. In this model, membrane curvature will help driving lipid sorting [43], and subsequent lipid clustering will contribute to protein sorting [5,7,8]. Therefore membrane curvature drives lipid and protein sorting. That such specific domains as for example the sterol-rich and sphingolipidrich domains are involved in intracellular protein transport was also shown in plant cells [44,45]. In addition, it was recently shown that reducing the lipid order of the Golgi membrane impaired vesicle fission and cargo export from the Golgi in animal cells [46]. Initiation of membrane domains can require phosphoinositides which have been found to be enriched in such domains in plant cells [47]. In animal cells, it was shown that the cytosolic PLA2e is recruited through interactions with phosphoinositides to initiate tubule formation [48]. The different PIP and PIP2 species have been extensively shown to be involved in several aspects of membrane trafficking in plant cells [49,50,51,52 and references therein]. Moreover, according to the effects observed in pi4k1/pi4k2 knockout double mutants, PI-4Kb1/PI-4Kb2 kinases could regulate the formation and the size of secretory vesicles at the TGN [53]. Many studies have pointed out that phosphoinositides and kinases involved in their biosynthesis are involved in PIN proteins polar localization, patterning, lateral root formation and root gravitropism in Arabidopsis. Moreover, the recent discovery that auxin regulates the amounts of PIP and PIP2 at the plasma membrane, coupled to the established fact that phosphoinositides have an effect on PIN proteins polarity and auxin distribution, introduces the concept of a regulatory loop [52]. In addition, it was shown that over-expression of PIS1 and PIS2 (involved in the biosynthesis of phosphatidylinositol from which PIP and PIP2 are formed) also induces the synthesis of PA and that over-expression of PIS1 also induces the synthesis of Current Opinion in Plant Biology 2014, 22:22–29

PE and DAG [54]. It has also been determined that PIS2 is involved in the synthesis of phosphatidylinositol molecular species from which are synthesized phosphoinositides species implicated in the regulation of the secretory pathway, as shown for pectin secretion in pollen tubes [55]. Moreover it was shown that lipids, including phosphoinositides, can be sorted and therefore concentrated in different membrane domains according to their fatty acyl chains in animal cells [56,57]. In the case of phosphoinositides, this membrane domain sorting is also dependent to their polar head (number of phosphate groups), and it contributes to their membrane mobility in animal cells [57]. Finally, from membrane models, it has also to be taken into account that the recruitment and activity of specific enzymes such as a PI-specific PLC can be highly dependent on membrane curvature/order [58]. Altogether these points indicate how complex must be the multi-step regulation of lipid synthesis/segregation, lipid-protein interactions, membrane dynamics and membrane domain homeostasis which are linked to protein trafficking and polarity in plant cells. Consistently, a specific ER-derived compartment where PI synthesis is concentrated was identified in animal cells and could regulate delivery of phosphoinositides to other membranes [59]. English and Voeltz [60] have recently characterized that such a compartment in animal cells is enriched in CEPT1 which convert DAG into PE and PC, and that the GTPase Rab10 regulates the formation of this dynamic domain. These combined protein and lipid machineries could either manage ER tubule extension and fusion [60] or help the transfer of specific lipids from these ER tubules to other membranes in close contact [59,60]. Whether such specialized ER-derived compartments exist in plant cells will be a challenge to meet. Pioneering studies in plant cells showed that glycerol-3phosphate acyltransferases and diacylglycerol acyltransferases associate in specific ER sub-domains through protein–protein interactions [61]. Finally, lipid–protein interactions through specific recognition of particular lipid species by proteins of the vesicle formation machinery have been shown to be crucial to control the overall process in animal and yeast cells [7,62,63,64,65]. Consistently, Contreras et al. [65] found a specific interaction between the transmembrane domain of p24, a protein of COPI machinery, and a particular species of sphingomyelin, demonstrating how very specific lipid-protein interactions can be. All the studies performed in various eukaryotic models (including plant systems) clearly point out the highly complex and tightly regulated biochemical/biophysical mechanisms which are involved in governing membrane morphodynamics and the secretory/retrograde pathways. Deciphering the roles of different lipid families and www.sciencedirect.com

Endomembranes morphodynamics and lipid diversity Boutte´ and Moreau 27

specific lipid molecular species in these processes in plant cells will be a tremendous challenge in the future.

6.

Melser S, Molino D, Batailler B, Peypelut M, Laloi M, WatteletBoyer V, Bellec Y, Faure JD, Moreau P: Links between lipid homeostasis, organelle morphodynamics and protein trafficking in eukaryotic and plant secretory pathways. Plant Cell Rep 2011, 30:177-193 (Erratum in Plant Cell Rep 2011, 30:675–676).

7.

Bankaitis VA, Garcia-Mata R, Mousley CJ: Golgi membrane dynamics and lipid metabolism. Curr Biol 2012, 22:R414-R424.

8.

Surma MA, Klose C, Simons K: Lipid-dependent protein sorting at the trans-Golgi network. Biochim Biophys Acta 2012, 1821:1059-1067.

9.

Voeltz GK, Prinz WA: Sheets, ribbons and tubules-how organelles get their shape. Nature 2007, 8:258-264.

Concluding remarks and perspectives Understanding of lipid-dependent mechanisms in endomembrane morphodynamics remains at its early stages. From one side, Surma et al. [66] found that secretory vesicles immunoisolated from three different cargo proteins had very similar lipid compositions (sphingolipids and ergosterol enrichment), suggesting a generic lipid-dependent mechanism for the formation of carrier vesicles from the Golgi in yeast. On another side, it is known that the transport of different proteins could rely on distinct lipids and therefore probably different carriers [8]. In the future, it will be therefore a challenge to unravel all the levels of interfaces between lipid and protein machineries (Figure 2). Plants are particularly good models to study lipids–proteins interconnections due to that plants quickly react to a change within the environment and the associated cellular processes are strongly relying on the plasticity of the secretory/retrograde pathways. High throughput screening will help in deciphering the metabolic pathways and key molecules involved [67]. In addition, specific tools for profiling lipid–protein interactions in vivo will be helpful to establish and build a lipid–protein interactome [68,69]. Finally, the need to visualize lipid molecules, lipid– protein interactions and lipid domains through different approaches [69–75] will be valuable tools for understanding the roles of lipids and their metabolism in the regulation of the secretory/retrograde pathways.

Acknowledgments This work was sustained by CNRS (Centre National de la Recherche Scientifique) and the University of Bordeaux.

References and recommended reading Papers of particular interest, published within the period of review, have been highlighted as:  of special interest  of outstanding interest

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40. Sebastian TT, Baldridge RD, Xu P, Graham TR: Phospholipid flippases: building asymmetric membranes and transport vesicles. Biochim Biophys Acta 2012, 1821:1068-1077.

25. Li G, Xue HW: Arabidopsis PLDz2 regulates vesicle trafficking and is required for auxin response. Plant Cell 2007, 19:281-295.

41. Xu H, Su W, Cai M, Jiang J, Zeng X, Wang H: The asymmetrical structure of Golgi apparatus membranes revealed by in situ atomic force microscope. PLoS One 2013, 8:e61596.

26. Pleskot R, Pejchar P, Bezvoda R, Lichtscheidl IK, Wolters-Arts M,  Marc J, Zarsky V, Potocky M: Turnover of phosphatidic acid through distinct signaling pathways affects multiple aspects of pollen tube growth in tobacco. Front Plant Sci 2012, 3:54. This study highlights the central role of phosphatidic acid (PA) and enzymes of its metabolism in several aspects of pollen tube growth. The homeostasis of PA through the different metabolic pathways seems to indicate that different pools of PA may exist. These different pools would be involved in the regulation of distinct events of pollen tube growth. 27. Sarri E, Sicart A, Lazaro-Dieguez F, Egea G: Phospholipid synthesis participates in the regulation of diacylglycerol required for membrane trafficking at the Golgi complex. J Biol Chem 2011, 286:28632-28643. 28. Men S, Boutte´ Y, Ikeda Y, Li X, Palme K, Stierhof YD, Hartmann MA, Moritz T, Grebe M: Sterol-dependent endocytosis mediates post-cytokinetic acquisition of PIN2 auxin efflux carrier polarity. Nat Cell Biol 2008, 10:237-244. 29. Boutte´ Y, Frescatada-Rosa M, Men S, Chow CM, Ebine K, Gustavsson A, Johansson L, Ueda T, Moore I, Ju¨rgens G: Grebe endocytosis restricts Arabidopsis KNOLLE syntaxin to the cell division plane during late cytokinesis. EMBO J 2010, 29:546-558.

42. Poulsen LR, Lopez-Marque´z RL, McDowell SC, Okkeri J, Licht D, Schulz A, Pomorski T, Harper JF, Palmgren MG: The Arabidopsis P4-ATPase ALA3 localizes to the Golgi and requires a bsubunit to function in lipid translocation and secretory vesicle formation. Plant Cell 2008, 20:658-676. 43. Sorre B, Callan-Jones A, Manneville JB, Nassoy P, Joanny JF, Prost J, Goud B, Bassereau P: Curvature-driven lipid sorting needs proximity to a demixing point and is aided by proteins. Proc Natl Acad Sci USA 2009, 106:5622-5626. 44. Laloi M, Perret AM, Chatre L, Melser S, Cantrel C, Vaultier MN, Zachowski A, Bathany K, Schmitter JM, Vallet M et al.: Insights into the role of specific lipids in the formation and delivery of lipid microdomains to the plasma membrane of plant cells. Plant Physiol 2007, 143:1-12. 45. Cacas JL, Furt F, Le Gue´dard M, Schmitter JM, Bure´ C, Gerbeau-Pissot P, Moreau P, Bessoule JJ, Simon-Plas F, Mongrand S: Lipids of plant membrane rafts. Prog Lipid Res 2012, 51:272-299.

30. MZhou Y, Peisker H, Weth A, Baumgartner W, Do¨rmann P, Frentzen M: Extraplastidial cytidinediphosphate diacylglycerol synthase activity is required for vegetative development in Arabidopsis thaliana. Plant J 2013, 75:867-879.

46. Duran JM, Campelo F, van Galen J, Sachsenheimer T, Sot J,  Egorov MV, Rentero C, Enrich C, Polishchuk RS, Goni FM et al.: Sphingomyelin organization is required for vesicle biogenesis at the Golgi complex. EMBO J 2012, 31:4535-4546. This work clearly illustrates how lipid biosynthesis impacts membrane domain organization/lipid order and mediates membrane curvature which in turn influences the efficiency of vesicle formation at the Golgi complex in animal cells.

31. Luo Y, Qin G, Zhang J, Liang Y, Song Y, Zhao M, Tsuge T, Aoyama T, Liu J, Gu H, Qu LJ: D-myo-inositol-3-phosphate affects phosphatidylinositol-mediated endomembrane function in Arabidopsis and is essential for auxin-regulated embryogenesis. Plant Cell 2011, 23:1352-1372.

47. Furt F, Ko¨nig S, Bessoule JJ, Sargueil F, Zallot R, Stanislas T, Noirot E, Lherminier J, Simon-Plas F, Heilmann I, Mongrand S: Polyphosphoinositides are enriched in plant membrane rafts and form microdomains in the plasma membrane. Plant Physiol 2010, 152:2173-2187.

32. Eastmond PJ, Quettier AL, Kroon JTM, Craddock C, Adams N, Slabas AR: Phosphatidic acid phosphohydrolase 1 and 2 regulate phospholipid synthesis at the endoplasmic reticulum in Arabidopsis. Plant Cell 2010, 22:2796-2811.

48. Capestrano M, Mariggio S, Perinetti G, Egorova AV, Iacobacci S, Santoro M, Di Pentima A, Iurisci C, Egorov MV, Di Tullio G, Buccione R, Luini A, Polishchuk RS: Cytosolic phospholipase A2e drives recycling through the clathrin-independent endocytic route. J Cell Sci 2014, 127:977-993.

33. Melser S, Batailler B, Peypelut M, Poujol C, Bellec Y, WatteletBoyer V, Maneta-Peyret L, Faure JD, Moreau P: Glucosylceramide biosynthesis is involved in Golgi morphology and protein secretion in plant cells. Traffic 2010, 11:479-490. 34. Markham JE, Lynch DV, Napier JA, Dunn TM, Cahoon EB: Plant sphingolipids: function follows form. Curr Opin Plant Biol 2013, 16:350-357. 35. Roudier F, Gissot L, Beaudoin F, Haslam R, Michaelson L, Marion J, Molino D, Lima A, Bach L, Morin H et al.: Very-longchain fatty acids are involved in polar auxin transport and developmental patterning in Arabidopsis. The Plant Cell 2010, 22:364-375. Current Opinion in Plant Biology 2014, 22:22–29

49. Munnik T, Nielsen E: Green light for polyphosphoinositide signals in plants. Curr Op Plant Biol 2011, 14:489-497. 50. Mei Y, Jia WJ, Chu YJ, Xue HW: Arabidopsis  phosphatidylinositol monophosphate 5-kinase 2 is involved in root gravitropism through regulation of polar auxin transport by affecting the cycling of PIN proteins. Cell Res 2012, 22:581-597. A knockout mutant of PIP5K2 shows reduced lateral root formation, suppression of PIN2 and PIN3 proteins cycling and a delayed redistribution of PIN2 and auxin under gravistimulation. The results strongly suggest that PIP5K2 is involved in regulating lateral root formation and root gravitropism through regulation of PIN proteins and polar auxin transport. www.sciencedirect.com

Endomembranes morphodynamics and lipid diversity Boutte´ and Moreau 29

51. Ischebeck T, Werner S, Krishnamoorthy P, Lerche J, Meijo´n M,  Stenzel I, Lo¨fke C, Wiessner T, Im YJ, Perera IY et al.: Phosphatidylinositol 4,5-bisphosphate influences PIN polarization by controlling clathrin-mediated membrane trafficking in Arabidopsis. Plant Cell 2013, 25:4894-4911. Following precedent studies on the role of phosphoinositides in plant cell physiology, Heilmann and coworkers have shown that phosphoinositide metabolism is a strong regulator of clathrin-mediated endocytosis and also show that phosphoinositide metabolism has an effect on PIN proteins polarization and auxin distribution.

63. Maeda K, Anand K, Chiapparino A, Kumar A, Poletto M, Kaksonen M, Gavin AC: Interactome map uncovers phosphatidylserine transport by oxysterol-binding proteins. Nature 2013, 501:257-261.

52. Tejos R, Sauer M, Vanneste S, Palacios-Gomez M, Li H,  Heilmann M, van Wijk R, Vermeer JE, Heilmann I, Munnik T, Friml J: Bipolar plasma membrane distribution of phosphoinositides and their requirement for auxin-mediated cell polarity and patterning in Arabidopsis. Plant Cell 2014, 26:2114-2128. The authors have deciphered more deeply the polar distribution of phosphoinositides and PI kinases and its role in cell polarity and patterning in Arabidopsis. They have shown that PI4P, PI(4,5)P2, and the kinases PIP5K1 and PIP5K2 have different polarities. They also show that auxin can regulate the amounts of PI4P and PI(4,5)P2 at the plasma membrane. Since phosphoinositides have an effect on PIN proteins polarization and auxin distribution, the concept of a regulatory loop is emerging from their work.

65. Contreras FX, Ernst AM, Haberkant P, Bjo¨rkholm P, Lindahl E,  Go¨nen B, Tischer C, Elofsson A, von Heijne G, Thiele C et al.: Molecular recognition of a single sphingolipid species by a protein’s transmembrane domain. Nature 2012, 481:525-529. This study reports for the first time in animal cells the specific interaction of a unique sphingolipid molecular species with the transmembrane domain of p24, a protein involved in the biogenesis of COPI vesicles. The authors show that this interaction triggers p24 dimerization and affect protein transport. With this work, the authors reveal that similar specific interactions exist between distinct lipid molecular species and various proteins. Therefore an inherent complexity of lipid-protein interactions must exist to regulate membrane dynamics and functions.

53. Kang BH, Nielsen E, Preuss ML, Mastronarde D, Staehelin LA: Electron tomography of RabA4b- and PI-4Kb1-labeled trans Golgi network compartments in Arabidopsis. Traffic 2011, 12:313-329. 54. Lo¨fke C, Ischebeck T, Ko¨nig S, Freitag S, Heilmann I: Alternative metabolic fates of phosphatidylinositol produced by phosphatidylinositol synthase isoforms in Arabidopsis thaliana. Biochem J 2008, 413:115-124. 55. Ischebeck T, Vua LH, Jina X, Stenzela I, Lo¨fke C, Heilmann I: Functional cooperativity of enzymes of phosphoinositide conversion according to synergistic effects on pectin secretion in tobacco pollen tubes. Mol Plant 2010, 3:870-881. 56. Mukherjee S, Soe TT, Maxfield FR: Endocytic sorting of lipid analogues differing solely in the chemistry of their hydrophobic tails. J Cell Biol 1999, 144:1271-1284. 57. Cho H, Kim YA, HOWK: Phosphate number and acyl chain length determine the subcellular location and lateral mobility of phosphoinositides. Mol Cells 2006, 22:97-103. 58. Ahyayauch H, Villar AV, Alonso A, Gon˜i FM: Modulation of PI-specific phospholipase C by membrane curvature and molecular order. Biochemistry 2005, 44:11592-11600. 59. Kim YJ, Guzman-Hernandez ML, Balla T: A highly dynamic  ER-derived phosphatidylinositol-synthesizing organelle supplies phosphoinositides to cellular membranes. Dev Cell 2011, 21:813-824. This work evidences, for the first time in animal cells, the possible existence of a specialized ER-derived organelle which is particularly involved in the biosynthesis of phosphoinositides. In addition, this organelle could regulate the supply of phosphoinositides to several other membrane compartments by direct interactions. 60. English AR, Voeltz GK: Rab10 GTPase regulates ER dynamics  and morphology. Nat Cell Biol 2013, 15:169-178. The Rab10 GTPase is shown to be involved in the efficiency of ER tubule extension and fusion in animal cells. Rab10 is found to be located at specific dynamic domains from where new tubules grow. In addition, these domains were also characterized by the concentration of two enzymes of phospholipid biosynthesis (PIS and CEPT1) required respectively for phosphatidylinositol and phosphatidylethanolamine/phosphatidylcholine synthesis. These results suggest that Rab10-mediated ER tubule extension and fusion are coupled to de novo phospholipid biosynthesis. 61. Gidda SK, Shockey JM, Falcone M, Kim PK, Rothstein SJ, Andrews DW, Dyer JM, Mullen RT: Hydrophobic-domaindependent protein-protein interactions mediate the localization of GPAT enzymes to ER subdomains. Traffic 2011, 12:452-472. 62. Klinkenberg D, long KR, Shome K, Watkins SC, Aridor M: A cascade of ER exit site assembly that is regulated by p125A and lipid signals. J Cell Sci 2014, 127:1765-1778.

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64. Kajiwara K, Ikedo A, Aguilera-Romero A, Castillon GA, Kagiwada S, Hanada K, Riezman H, Muniz M, Funato K: Osh proteins regulate COPII-mediated vesicular transport of ceramide from the endoplasmic reticulum in budding yeast. J Cell Sci 2014, 127:376-387.

66. Surma MA, Klose C, Klemm RW, Ejsing CS, Simons K: Generic sorting of raft lipids into secretory vesicles in yeast. Traffic 2011, 12:1139-1147. 67. Zauber H, Burgos A, garapati P, Schulze WX: Plasma membrane lipid-protein interactions affect signaling processes in sterolbiosynthesis mutants in Arabidopsis thaliana. Front Plant Sci 2014, 5:78. 68. McLoughlin F, Arisz SA, Dekker HL, Kramer G, de Koster CG,  Haring MA, Munnik T, Testerink C: Identification of novel candidate phosphatidic acid-binding proteins involved in the salt-stress response of Arabidopsis thaliana roots. Biochem J 2013, 450:573-581. This work identified several phosphatidic acid-binding proteins which could be involved in the salt-stress response in Arabidopsis thaliana. Interestingly, some proteins (clathrin heavy chain and clathrin assembly proteins) are involved in the regulation of clathrin-mediated endocytosis and other intracellular events. Therefore these results suggest again the potential crucial effect of lipid–protein interactions on the regulation of membrane dynamics. 69. Haberkant P, Raijmakers R, Wildwater M, Sachsenheimer T, Bru¨gger B, Maeda K, Houweling M, Gavin AC, Schultz C, van Meer G, Heck AJR, Holthuis JCM: In vivo profiling and visualization of cellular protein–lipid interactions using bifunctional fatty acids. Angew Chem Int Ed 2013, 52:4033-4038. 70. Blachutzik JO, Demir F, Kreuzer I, Hedrich R, Harms GS: Methods of staining and visualization of sphingolipid enriched and nonenriched plasma membrane regions of Arabidopsis thaliana with fluorescent dyes and lipid analogues. Plant Methods 2012, 8:28. 71. Honigmann A, Mueller V, Hell SW, Eggeling C: STED microscopy detects and quantifies liquid phase separation in lipid membranes using a new far-red emitting fluorescent phosphoglycerolipid analogue. Faraday Discuss 2013, 161:77-89. 72. Owen DM, Gaus K: Imaging lipid domains in cell membranes: the advent of super-resolution fluorescence microscopy. Front Plant Sci 2013, 4:503. 73. Simon MLA, platre MP, Assil S, van Wijk R, Chen WY, Chory J, Dreux M, Munnik T, Jaillais Y: A multi-colour/multi-affinity marker set to visualize phosphoinositide dynamics in Arabidopsis. Plant J 2014, 77:322-337. 74. Potocky´ M, Pleskot R, Pejchar P, Vitale N, Kost B, Za´rsky´ V: Livecell imaging of phosphatidic acid dynamics in pollen tubes visualized by Spo20p-derived biosensor. New Phytol 2014. doi:10.1111/nph.12814. 75. Peddie CJ, Blight K, Wilson E, Melia C, Marrison J, Carzaniga R, Domart MC, O’Toole P, Larijani B, Collinson LM: Correlative and integrated light and electron microscopy of in-resin GFP fluorescence, used to localize diacylglycerol in mammalian cells. Ultramicroscopy 2014, 143:3-14.

Current Opinion in Plant Biology 2014, 22:22–29